Version .

0 20
TINKER
Software Tools for Molecular Design












TINKER





Software Tools for Molecular Design
Version 6.0
October 2011















Copyright 1990-2011 by Jay William Ponder
All Rights Reserved

2 TINKER User's Guide 2














Copyright 1990-2011 by Jay William Ponder
All Rights Reserved


User's Guide Cover Illustration by Jay Nelson
Courtesy of Prof. R. T. Paine, Univ. of New Mexico


TINKER IS PROVIDED "AS IS" AND WITHOUT ANY WARRANTY
EXPRESS OR IMPLIED. THE USER ASSUMES ALL RISKS OF
USING THIS SOFTWARE. THERE IS NO CLAIM OF THE
MERCHANTABILITY OR FITNESS FOR A PARTICULAR
PURPOSE.

YOU MAY MAKE COPIES OF TINKER FOR YOUR OWN USE,
AND MODIFY THOSE COPIES. YOU MAY NOT DISTRIBUTE ANY
MODIFIED SOURCE CODE OR DOCUMENTATION TO USERS AT
ANY SITE OTHER THAN YOUR OWN. PLEASE SIGN AND
RETURN THE TINKER LICENSE AGREEMENT IF YOU MAKE
USE OF THIS SOFTWARE.


V6.0 10/11
3 TINKER User's Guide 3


TINKER

Software Tools for Molecular Design
Version 6.0 October 2011


Table of Contents Page

1. Introduction to the Software 5
2. Installation on your Computer 7
3. Types of Input & Output Files 10
4. Potential Energy Programs 13
5. Additional Utility Programs & Scripts 19
6. Special Features & Methods 23
7. Use of the Keyword Control File 29
8. Force Field Parameter Sets 61
9. Descriptions of Source Routines 69
10. Descriptions of Global Variables 139
11. Index of Function & Subroutine Calls 167
12. Test Cases & Examples 196
13. Benchmark Results 198
14. Collaborators & Acknowledgments 202
15. References & Suggested Reading 204

4 "#$%&' ()*+,) -./0* 4

5 "#$%&' ()*+,) -./0* 5
12 #34+50.64/53 45 47* 8594:;+*
<7;4 /) 47* "#$%&' 8594:;+*=
Welcome to the TINKER moleculai moueling package! TINKER is uesigneu to be an easily useu anu
flexible system of piogiams anu ioutines foi moleculai mechanics anu uynamics as well as othei
eneigy-baseu anu stiuctuial manipulation calculations. It is intenueu to be mouulai enough to enable
uevelopment of new computational methous anu efficient enough to meet most piouuction
calculation neeus. Rathei than incoipoiating all the functionality in one monolithic piogiam, TINKER
pioviues a set of ielatively small piogiams that inteiopeiate to peifoim complex computations. New
piogiams can be easily auueu by moueleis with only limiteu piogiamming expeiience.
>*;4.+*) ;30 ?;@;A/B/4/*)
The seiies of majoi piogiams incluueu in the uistiibution system peifoim the following coie tasks:

(1) builuing piotein anu nucleic aciu mouels fiom sequence
(2) eneigy minimization anu stiuctuial optimization
(S) analysis of eneigy uistiibution within a stiuctuie
(4) moleculai uynamics anu stochastic uynamics
(S) simulateu annealing with a choice of cooling scheuules
(6) noimal moues anu vibiational fiequencies
(7) confoimational seaich anu global optimization
(8) tiansition state location anu confoimational pathways
(9) fitting of eneigy paiameteis to ciystal uata
(1u) uistance geometiy with paiiwise metiization
(11) moleculai volumes anu suiface aieas
(12) fiee eneigy changes foi stiuctuial mutations
(1S) auvanceu algoiithms baseu on potential smoothing

Nany of the vaiious eneigy minimization anu moleculai uynamics computations can be peifoimeu
on full oi paitial stiuctuies, ovei Caitesian, inteinal oi iigiu bouy cooiuinates, anu incluuing a vaiiety
of bounuaiy conuitions anu ciystal cell types. 0thei piogiams aie available to geneiate timing uata
anu allow checking of potential function ueiivatives foi couing eiiois. Special featuies aie available
to facilitate input anu output of piotein anu nucleic aciu stiuctuies. Bowevei, the basic coie ioutines
have no knowleuge of biopolymei stiuctuie anu can be useu foi geneial moleculai systems.

Bue to its emphasis on ease of mouification, TINKER uiffeis fiom many othei cuiiently available
moleculai moueling packages in that the usei is expecteu to be willing to wiite simple ``fiont-enu''
piogiams anu make some alteiations at the souice coue level. The main piogiams pioviueu shoulu
be consiueieu as templates foi the useis to change accoiuing to theii wishes. All subioutines aie
inteinally uocumenteu anu stiuctuieu piogiamming piactices aie auheieu to thioughout. The iesult,
it is hopeu, will be a calculational system which can be tailoieu to local neeus anu uesiies.

The coie TINKER system consists of neaily 1SS,uuu lines of souice wiitten entiiely in a poitable
Foitian77 supeiset. 0se is maue of only some veiy common extensions that aiu in wiiting highly
stiuctuieu coue. The cuiient veision of the package has been poiteu to a wiue iange of computeis
with no oi extiemely minimal changes. Testeu systems incluue: Reu Bat Linux, Niciosoft Winuows
9XNT2uuuXP, Apple 0S9 anu 0SX, BPCompaqBEC Alphas unuei Tiu64 0nix anu 0penvNS,
Bewlett-Packaiu, IBN, Silicon uiaphics anu Sun woikstations unuei each venuoi's 0nix. At piesent,
oui new coue is wiitten on vaiious Linux platfoims, anu occasionally testeu foi compatibility on
6 "#$%&' ()*+,) -./0* 6
vaiious of the othei machine anu 0S combinations listeu above. At piesent, we aie in the piocess of
conveiting oui piimaiy uevelopment effoits fiom Foitian77 to a moie mouein Foitian uialect. A
machine-tianslateu C veision of TINKER is cuiiently available, anu a hanu-tianslateu optimizeu C
veision of a pievious TINKER ielease is available foi inspection. Conveision to C oi C++ is unuei
consiueiation, but not being actively puisueu at this time.

The basic uesign of the eneigy function engine useu by the TINKER system allows usage of seveial
uiffeient paiametei sets. At piesent we aie uistiibuting paiameteis that implement ANBER ff94 anu
ff96, CBARNN19 anu 27, NN2, NNS, 0PLS-0A, 0PLS-AA, Liam Bang's polaiizable potentials, anu oui
own AN0EBA (Atomic Nultipole 0ptimizeu Eneigetics foi Biomoleculai Applications) paiameteis. In
most cases, the souice coue sepaiates the geometiic manipulations neeueu foi eneigy ueiivatives
fiom the actual foim of the eneigy function itself. Seveial othei liteiatuie paiametei sets aie being
consiueieu foi possible futuie uevelopment (ENCAB, NNFF-94, NN4, 0FF, !"#$%, anu many of the
alteinative potential function foims iepoiteu in the liteiatuie can be implementeu uiiectly oi aftei
minoi coue changes.

Nuch of the softwaie in the TINKER package has been heavily useu anu well testeu, but some
mouules aie still in a faiily eaily stage of uevelopment. Fuithei woik on the TINKER system is
planneu in thiee main aieas: (1) extension anu impiovement of the potential eneigy paiameteis
incluuing auuitional paiameteiization anu testing of oui polaiizable multipole AN0EBA foice fielu,
(2) couing of new computational algoiithms incluuing auuitional methous foi fiee eneigy
ueteimination, toisional Nonte Cailo anu moleculai uynamics sampling, auvanceu methous foi long
iange inteiactions, bettei tiansition state location, anu fuithei application of the potential smoothing
paiauigm, anu (S) fuithei uevelopment of Foice Fielu Exploiei, a }ava-baseu u0I fiont-enu to the
TINKER piogiams that pioviues foi calculation setup, launch anu contiol as well as basic moleculai
visualization.
?534;64 #395+C;4/53

Questions anu comments iegaiuing the TINKER package, incluuing suggestions foi impiovements
anu changes shoulu be maue to the authoi:

Piofessoi }ay William Ponuei
Bepaitment of Chemistiy, Box 11S4
Washington 0niveisity in Saint Louis
0ne Biookings Ball
Saint Louis, N0 6S1Su 0.S.A.

office: Louueiman Ball, Room 4SS
phone: (S14) 9SS-427S
fax: (S14) 9SS-4481
email: ponueiuashei.wustl.euu

In auuition, an Inteinet web site containing an online veision of this 0sei's uuiue, the most iecent
uistiibution veision of the full TINKER package anu othei useful infoimation can be founu at
http://dasher.wustl.edu/tinker, the Bome Page foi the TINKER Noleculai Noueling
Package.

7 "#$%&' ()*+,) -./0* 7
D2 #3)4;BB;4/53 53 E5.+ ?5C@.4*+
How to Obtain a Copy of TINKER

The TINKER package is uistiibuteu on the Inteinet via eithei the web site oi the anonymous ftp
account on dasher.wustl.eduwith an IP numbei of 128.2S2.2u8.48. This noue is a web anu file
seivei locateu in the Ponuei lab at Washington 0niveisity School of Neuicine. The package is
available via the web anu stanuaiu biowseis fiom the TINKER home page at
http://dasher.wustl.edu/tinker/. Alteinatively TINKER can be uownloaueu by logging
into dasher.wustl.eduvia anonymous ftp (0seiname: anonymous, Passwoiu: Fyour email
addressF) anu uownloauing the softwaie fiom the pubtinkei subuiiectoiy. The complete TINKER
uistiibutions as well as inuiviuual files can be uownloaueu fiom this site.

The easiest way to get TINKER iunning on youi machine is to use the self-extiacting installation kit
foi eithei Linux, Winuows, oi Nacintosh 0S X 1u.S. The installei will guiue you thiough complete
setup of TINKER anu the Foice Fielu Exploiei (FFE) u0I, anu peifoim all iequiieu configuiation
choies. The installei kits foi the thiee suppoiteu systems aie tinker4.2-linux.sh,
tinker4.2-windows.exeanu tinker4.2-macosx.sit. The Linux anu Winuows kits each
contain a piivate copy of a }ava anu }avaSB iun-time enviionment foi use with the package. The
Nacintosh veision iequiies an 0S X 1u.S (Panthei) system foi installation. The native }ava
implementation is useu on Nacs, anu the }avaSB package must be uownloaueu fiom Apple anu
installeu piioi to using TINKER with Foice Fielu Exploiei.
G+*A./B4 "#$%&' &H*6.4;AB*)

The TINKER package is also available as compiesseu 0nix tai aichives, Winuows zip files, anu as a
complete set of uncompiesseu souice anu uata files. Binaiies aie pioviueu foi machines iunning
Winuows 9XNENT2uuuXP, Linux, anu Apple Nac 0S X. All of these executables aie piesent in
stanuaiu compiesseu foimats as inuiviuual piogiams oi as complete sets of executables. It is
expecteu that othei 0nix useis anu PC useis who neeu specially customizeu veisions, will builu
binaiies foi theii specific system. Sites with access to the 0nix tai, compiess anu uncompiess
commanus shoulu simply obtain the aichive file tinker.tar.Z. Alteinatively, tinker.tar.gz
anu tinker.zip containing iuentical uistiibutions compiesseu to uN0 gzip anu Winuows ZIP
foimat aie also pioviueu. If you choose to uownloau inuiviuual files, you will neeu at a minimum the
contents of the uoc, souice anu paiams subuiiectoiies. Also iequiieu aie the compilebuilu
sciipts fiom the subuiiectoiy nameu foi youi machine type. 0thei aieas contain test cases anu
examples, benchmaik iesults, machine-tianslateu C coue, anu the Foice Fielu Exploiei }ava u0I foi
TINKER. The entiie TINKER package, aftei builuing the executables, will iequiie fiom about 4u to
ovei 1Su megabytes of uisk space uepenuing on the components installeu anu the use of shaieu
libiaiies in the executables.

Building your Own Executables
The compilation anu builuing of the TINKER executables shoulu be easy foi most of the common
woikstation anu PC class computeis. We pioviue in the make aiea a 0nix-style Nakefile that with
some mouification can be useu to builu TINKER on most 0nix machines. As a simplei alteinative to
Nakefiles foi the 0nix veisions, we also pioviue machine-specific uiiectoiies with thiee sepaiate
shell sciipts to compile the souice, builu an object libiaiy, anu link binaiy executables. Thiee similai
commanu files aie pioviueu foi Winuows, Nacintosh anu 0pen vNS systems. Compilation on 0nix
woikstations shoulu use the venuoi supplieu Foitian compilei, if available. The public uomain uN0
8 "#$%&' ()*+,) -./0* 8
g77 Foitian compilei available fiom http://gcc.gnu.org/is also capable of builuing TINKER
on Linux anu othei 0nix-baseu machines. The Linux executables we pioviue aie built with the Intel
Foitian foi Linux 8.u compilei. The Poitlanu uioup (PuI) anu Absoft PioFoitian compileis have also
been testeu unuei Linux, both of which geneiate executables ioughly compaiable in speeu to the
Intel compilei. 0n Linux, the g77 executables tenu to exhibit uegiaueu peifoimance compaieu with
executables fiom commeicial compileis. Some benchmaik iesults aie pioviueu in a latei section of
this 0sei's uuiue Foi the Nacintosh we uistiibute executables built unuei Apple 0S X 1u.S with the
uN0 g77 compilei. TINKER also builus on the Nacintosh using the Absoft PioFoitian compilei. Foi
PCs iunning Winuows 9XNT2uuuXP, the uistiibuteu TINKER executables aie built unuei the Intel
Foitian foi Winuows 8.u compilei. Alteinative Winuows compileis such as Compaq visual Foitian,
LaheyFujitsu anu The Poitlanu uioup compileis, anu uN0 g77 unuei Cygwin have been testeu anu
shown to builu TINKER coiiectly. Please see the REABNE files in each of the machine-specific aieas
foi fuithei infoimation.

The fiist step in builuing TINKER using the sciipt files is to iun the appiopiiate
compile.make sciipt foi youi opeiating system anu compilei veision. Next you must use a
library.makesciipt to cieate an aichive of object coue mouules. Finally, iun a link.makesciipt
to piouuce the complete set of TINKER executables. The executables can be ienameu anu moveu to
wheievei you like by euiting anu iunning the ``iename'' sciipt. These steps will piouuce executables
that can iun fiom the commanu line, but without the capability to inteiact with the FFE u0I. Builuing
FFE-enableu TINKER executables involves ieplacing the sockets.fsouice file with sockets.c, anu
incluueu the object fiom the C coue in the TINKER object libiaiy. Then executables must be linkeu
against }ava libiaiies in auuition to the usual iesouices. Sample compgui.make anu
linkgui.makesciipts aie pioviueu foi systems capable of builuing u0I-enableu executables.

Regaiuless of youi taiget machine, only a few small pieces of coue can possibly iequiie
attention piioi to builuing. The fiist two aie the system uepenuent time anu uate ioutines founu in
clock.fanu calendar.fiespectively. Next is the openend.fioutine that facilitates appenuing
uata to the enu of an existing uisk file. Please uncomment the sections of these ioutines neeueu foi
youi computei type. veision of these system uepenuent ioutines suitable foi each system aie also
pioviueu in the uiiectoiy foi each machine0S type. The final set of possible souice alteiations aie to
the mastei aiiay uimensions founu in the incluue file sizes.i. The most basic limit is on the
numbei of atoms alloweu, ``maxatm''. This paiametei can be set to 1uuuu oi moie on most
woikstations. Peisonal computeis with minimal memoiy may neeu a lowei limit, peihaps 1uuu
atoms, uepenuing on available memoiy, swap space anu othei iesouices. A uesciiption of the othei
paiametei values is containeu in the heauei of the file. Note that in oiuei to keep the coue completely
tianspaient, TINKER uoes not implement any soit of uynamic memoiy allocation oi heap uata
stiuctuie. This iequiies that sizes.iuimensioning values be set at least as laige as the biggest
pioblem you intenu to iun. 0bviously, you shoulu not set the aiiay sizes to unnecessaiily laige
values, since this can tax youi compute iesouices anu may iesult in peifoimance uegiauation oi
oveit failuie of the executables.
I56.C*34;4/53 ;30 J47*+ #395+C;4/53

The uocumentation foi the TINKER piogiams, incluuing the guiue you aie cuiiently ieauing, is
locateu in the pubtinkeiuoc subuiiectoiy. The uocumentation was piepaieu using the Applixwaie
Woius anu uiaphics piogiams. Poitable veisions of the uocumentation aie pioviueu as ascii text in
.txtfiles anu in Auobe Aciobat .pdffile foimats. Please ieau anu ietuin by mail the TINKER
license. In paiticulai, we note that TINKER is not ``0pen Souice'' as useis aie piohibiteu fiom
ieuistiibution of oiiginal oi mouifieu TINKER souice coue oi binaiies to othei paities. While oui
intent is to uistiibute the TINKER coue to anyone who wants it, the Ponuei Lab woulu like to iemain
the sole uistiibution site anu keep tiack of ieseaicheis using the package. The ietuineu license foims
9 "#$%&' ()*+,) -./0* 9
also help us justify fuithei uevelopment of TINKER. When new mouules anu capabilities become
available, anu when the almost inevitable bugs aie uncoveieu, we will attempt to notify those who
have ietuineu a license foim. Finally, we ieminu you that this softwaie is copyiighteu, anu ask that it
not be ieuistiibuteu in any foim.
<7*+* 45 I/+*64 K.*)4/53)

Specific questions about the builuing oi use of the TINKER package shoulu be uiiecteu to
tinker@dasher.wustl.edu. TINKER ielateu questions oi comments of moie geneial inteiest
can be sent to the Computational Chemistiy List (http://www.ccl.net/) iun by }an Labanowski
at the 0niveisity of Notie Bame. The TINKER uevelopeis monitoi this list anu will iesponu to the list
oi the inuiviuual postei as appiopiiate.

10 "#$%&' ()*+,) -./0* 10
L2 "E@*) 59 #3@.4 MJ.4@.4 >/B*)
This section uesciibes the basic file types useu by the TINKER package. Let's say you wish to peifoim
a calculation on a paiticulai small oiganic molecule. Assume that the file name chosen foi oui input
anu output files is sample. Then all of the TINKER files will iesiue on the computei unuei the name
sample.xxxwheie .xxxis any of the seveial extension types to be uesciibeu below.

8NOGP&2QRS

The .xyzfile is the basic TINKER Caitesian cooiuinates file type. It contains a title line followeu by
one line foi each atom in the stiuctuie. Each line contains: the sequential numbei within the
stiuctuie, an atomic symbol oi name, X-, Y-, anu Z-cooiuinates, the foice fielu atom type numbei of
the atom, anu a list of the atoms connecteu to the cuiient atom. Except foi piogiams whose basic
opeiation is in toisional space, all TINKER calculations aie uone fiom some veision of the .xyz
foimat.

8NOGP&2#$"

The .intfile contains an inteinal cooiuinates iepiesentation of the moleculai stiuctuie. It consists
of a title line followeu by one line foi each atom in the stiuctuie. Each line contains: the sequential
numbei within the stiuctuie, an atomic symbol oi name, the foice fielu atom type numbei of the
atom, anu inteinal cooiuinates in the usual Z-matiix foimat. Foi each atom the inteinal cooiuinates
consist of a uistance to some pieviously uefineu atom, anu eithei two bonu angles oi a bonu angle
anu a uiheuial angle to pievious atoms. The length, angle anu uiheuial uefinitions uo not have to
iepiesent ieal bonueu inteiactions. Following the last atom uefinition aie two optional blank line
sepaiateu sets of atom numbei paiis. The fiist list contains paiis of atoms that aie covalently bonueu,
but whose bonu length was not useu as pait of the atom uefinitions. These paiis aie typically useu to
close iing stiuctuies. The seconu list contains ``bonus'' that aie to be bioken, &$!$, paiis of atoms that
aie not covalently bonueu, but which weie useu to uefine a uistance in the atom uefinitions.

8NOGP&2%&R

The keywoiu paiametei file always has the extension .keyanu is optionally piesent uuiing TINKER
calculations. It contains values foi any of a wiue vaiiety of switches anu paiameteis that aie useu to
change the couise of the computation fiom the uefault. The uetaileu contents of this file is explaineu
in a lattei section of this 0sei's uuiue. If a moleculai system specific keyfile, in this case
sample.key, is not piesent, the the TINKER piogiam will look in the same uiiectoiy foi a geneiic
file nameu tinker.key.

8NOGP&2IR$

The .dynfile contains values neeueu to iestait a moleculai oi stochastic uynamics computation. It
stoies the cuiient position, cuiient velocity anu cuiient anu pievious acceleiations foi each atom, as
well as the size anu shape of any peiiouic box oi ciystal unit cell. This infoimation can be useu to
stait a new uynamics iun fiom the final state of a pievious iun. 0pon staitup, the uynamics piogiams
always check foi the piesence of a .dynfile anu make use of it whenevei possible. The .dynfile is
upuateu concuiient with the saving of a new uynamics tiajectoiy snapshot.

8NOGP&2&$I

11 "#$%&' ()*+,) -./0* 11
The .end file type pioviues a mechanism to giacefully stop a iunning TINKER calculation. At
appiopiiate checkpoints uuiing a calculation, TINKER will test foi the piesence of a sample.end
file, anu if founu will teiminate the calculation aftei upuating the output. The .endfile can be
cieateu at any time uuiing a computation, anu will be uetecteu when the next checkpoint is ieacheu.
The file may be of zeio size, anu its contents aie unimpoitant. In the cuiient veision of TINKER, the
.endmechanism is only available within uynamics-baseu piogiams.

8NOGP&2TT1U 8NOGP&2TTDU 2222

Seveial types of computations piouuce files containing a thiee oi moie uigit extension (.001as
shown; oi .002, .137, .5678, !"#.). These aie iefeiieu to as cycle files, anu aie useu to stoie vaiious
types of output stiuctuies. The cycle files fiom a given computation aie iuentical in inteinal stiuctuie
to eithei the .xyzoi .intfiles uesciibeu above. Foi example, the vibiational analysis piogiam can
save the tenth noimal moue in sample.010. A moleculai uynamics-baseu piogiam might save its
tenth u.1 picoseconu fiame (oi an eneigy minimizei its tenth paitially minimizeu inteimeuiate) in a
file of the same name.

8NOGP&2PJ-

The Foice Fielu Exploiei inteiface to TINKER saves iesults of all calculations launcheu fiom the u0I
to a log file with the .logsuffix. Any output that woulu noimally be uiiecteu to the scieen aftei
staiting a piogiam fiom the commanu line is appenueu to this log file by Foice Fielu Exploiei.

8NOGP&2N'?

A TINKER aichive file is simply a seiies of .xyzCaitesian cooiuinate files appenueu togethei one
aftei anothei. This file can be useu to conuense the iesults fiom inteimeuiate stages of an
optimization, fiames fiom a moleculai uynamics tiajectoiy, oi set of noimal moue vibiations into a
single file foi stoiage. TINKER aichive files can be uisplayeu as ``movies'' by the Foice Fielu Exploiei
moueling piogiam.

8NOGP&2GIV

This file type contains cooiuinate infoimation in the PBB foimat uevelopeu by the Biookhaven
Piotein Bata Bank foi ueposition of mouel stiuctuies baseu on maciomoleculai X-iay uiffiaction anu
NNR uata. Although TINKER itself uoes not use .pdb files uiiectly foi inputoutput, auxiliaiy
piogiams aie pioviueu with the system foi inteiconveiting .pdb files with the .xyz foimat
uesciibeu above.

8NOGP&28&K

This file type contains the piimaiy sequence of a biopolymei in the stanuaiu one-lettei coue with Su
iesiuues pei line. The .seqfile foi a biopolymei is geneiateu automatically when a PBB file is
conveiteu to TINKER .xyzfoimat oi when using the PR0TEIN oi N0CLEIC piogiams to builu a
stiuctuie fiom sequence It is iequiieu foi the ieveise conveision of a TINKER file back to PBB
foimat..

8NOGP&2>'N?

The fiactional cooiuinates coiiesponuing to the asymmetiic unit of a ciystal unit cell aie stoieu in
the .fracfile. The inteinal foimat of this file is iuentical to the .xyzfile; except that the cooiuinates
aie fiactional insteau of in Angstiom units.
12 "#$%&' ()*+,) -./0* 12

8NOGP&2QOJP

The ARCBIvE piogiam has the option of conveiting a seiies of .xyzcycle files into an XNakemol
XYZ file. These files can be uisplayeu as a movie using the XNakemol uisplay piogiam. Note that the
.xmolfile foimat uoes not contain TINKER atom type infoimation, so it is not possible to conveit an
.xmolfile back into a TINKER .xyzfile.

8NOGP&2?N'

The ARCBIvE piogiam has the option of conveiting a seiies of .xyzcycle files into an Acceleiys
InsightII cooiuinate aichive file. These files can be uisplayeu as a movie using the InsightII uisplay
piogiam. Note that the .carfile foimat uoes not contain TINKER atom type infoimation, so it is not
possible to conveit a .carfile back into a TINKER .XYZfile.

GN'NO&"&' >#P&8

The potential eneigy paiametei files uistiibuteu with the TINKER package all enu in the extension
.prm, although this is not iequiieu by the piogiams themselves. Each of these files contains a
uefinition of the potential eneigy functional foims foi that foice fielu as well as values foi inuiviuual
eneigy paiameteis. Foi example, the mm3pro.prm file contains the eneigy paiameteis anu
uefinitions neeueu foi a piotein-specific veision of the NNS foice fielu.

13 "#$%&' ()*+,) -./0* 13
W2 G54*34/;B &3*+XE G+5X+;C)
This section of the manual contains a biief uesciiption of each of the TINKER potential eneigy
piogiams. A uetaileu example showing how to iun each piogiam is incluueu in a latei section. The
piogiams listeu below aie all pait of the main, suppoiteu uistiibution. Auuitional souice coue foi
vaiious unsuppoiteu piogiams can be founu in the othei uiiectoiy of the TINKER uistiibution.

NP?Y&OR

A simple piogiam to peifoim veiy basic fiee eneigy peituibation calculations. This piogiam is
pioviueu mostly foi uemonstiation puiposes. Foi example, we use ALCBENY in a moleculai
moueling couise laboiatoiy exeicise to peifoim such classic mutations as chloiiue to biomiue anu
ethane to methanol in watei. The piesent veision uses the peituibation foimula anu winuowing with
an explicit mapping of atoms involveu in the mutation (``ANBER''-style), insteau of theimouynamic
integiation anu inuepenuent fieely piopagating gioups of mutateu atoms (``CBARNN''-style). Some
of the coue specific to this piogiam is limiteu to the ANBER anu 0PLS potential functional foims, but
coulu be easily geneializeu to hanule othei potentials. A moie geneial anu sophisticateu veision is
cuiiently unuei uevelopment.

N$NPRS&

Pioviues infoimation about a specific moleculai stiuctuie. The piogiam will ask foi the name of a
stiuctuie file, which must be in the TINKER .xyzfile foimat, anu the type of analysis uesiieu.
0ptions allow output of: (1) total potential eneigy of the system, (2) bieakuown of the eneigy by
potential function type oi ovei inuiviuual atoms, (S) computation of the total uipole moment anu its
components, moments of ineitia anu iauius of gyiation, (4) listing of the paiameteis useu to compute
selecteu inteiaction eneigies, (S) eneigies associateu with specifieu inuiviuual inteiactions.

N$$&NP

Peifoims a moleculai uynamics simulateu annealing computation. The piogiam staits fiom a
specifieu input moleculai stiuctuie in TINKER .xyzfoimat. The tiajectoiy is upuateu using eithei a
mouifieu Beeman oi a velocity veilet integiation methou. The annealing piotocol is implementeu by
allowing smooth changes between staiting anu final values of the system tempeiatuie via the
uioningen methou of coupling to an exteinal bath. The scaling can be lineai oi sigmoiual in natuie. In
auuition, paiameteis such as cutoff uistance can be tiansfoimeu along with the tempeiatuie. The
usei must input the uesiieu numbei of uynamics steps foi both the equilibiation anu cooling phases,
a time inteival foi the uynamics steps, anu an inteival between cooiuinatetiajectoiy saves. All saveu
cooiuinate sets along the tiajectoiy aie placeu in sequentially numbeieu cycle files.

IR$NO#?

Peifoims a moleculai uynamics (NB) oi stochastic uynamics (SB) computation. Staits eithei fiom a
specifieu input moleculai stiuctuie (an .xyzfile) oi fiom a stiuctuie-velocity-acceleiation set saveu
fiom a pievious uynamics tiajectoiy (a iestait fiom a .dynfile). NB tiajectoiies aie piopagateu
using eithei a mouifieu Beeman oi a velocity veilet integiation methou. SB is implementeu via oui
own ueiivation of a velocity veilet-baseu algoiithm. In auuition the piogiam can peifoim full ciystal
calculations, anu can opeiate in constant eneigy moue oi with maintenance of a uesiieu tempeiatuie
anuoi piessuie using the uioningen methou of coupling to exteinal baths. The usei must input the
uesiieu numbei of uynamics steps, a time inteival foi the uynamics steps, anu an inteival between
cooiuinatetiajectoiy saves. Cooiuinate sets along the tiajectoiy can be saveu as sequentially
14 "#$%&' ()*+,) -./0* 14
numbeieu cycle files oi uiiectly to a TINKER aichive .arcfile. At the same time that a point along
the tiajectoiy is saveu, the complete infoimation neeueu to iestait the tiajectoiy fiom that point is
upuateu anu stoieu in the .dynfile.

-IN

A piogiam to implement Stiaub's uaussian Bensity Annealing algoiithm ovei an effective seiies of
analytically smootheu potential eneigy suifaces. This methou can be vieweu as an extenueu
stochastic veision of the uiffusion equation methou of Scheiaga, !" ()., anu also has many similai
featuies to the TINKER Potential Smoothing anu Seaich (PSS) seiies of piogiams. The cuiient
veision of uBA is similai to but uoes not exactly iepiouuce Stiaub's publisheu methou anu is limiteu
to aigon clusteis anu othei simple systems involving only van uei Waals inteiactions; fuithei
mouification anu uevelopment of this coue is cuiiently unueiway in the Ponuei ieseaich gioup. As
with othei piogiams involving potential smoothing, uBA cuiiently iequiies use of the smooth.prm
foice fielu paiameteis.

O#$#O#S&

The NININIZE piogiam peifoims a limiteu memoiy L-BFuS minimization of an input stiuctuie ovei
Caitesian cooiuinates using a mouifieu veision of the algoiithm of }oige Noceual. The methou
iequiies only the potential eneigy anu giauient at each step along the minimization pathway. It
iequiies stoiage space piopoitional to the numbei of atoms in the stiuctuie. The NININIZE
pioceuuie is iecommenueu foi pieliminaiy minimization of tiial stiuctuies to an *+, giauient of 1.u
to u.1 kcalmole-. It has a ielatively fast cycle time anu is toleiant of pooi initial stiuctuies, but
conveiges in a slow, lineai fashion neai the minimum. The usei supplies the name of the TINKER
.xyzcooiuinates file anu a taiget *+, giauient value at which the minimization will teiminate.
0utput consists of minimization statistics wiitten to the scieen oi ieuiiecteu to an output file, anu
the new cooiuinates wiitten to upuateu .xyzfiles oi to cycle files.

O#$#'J"

The NINIR0T piogiam uses the same limiteu memoiy L-BFuS methou as NININIZE, but peifoims
the computation in teims of uiheuial angles insteau of Caitesian cooiuinates. 0utput is saveu in an
upuateu .intfile oi in cycle files.

O#$'#-#I

The NINRIuIB piogiam is similai to NININIZE except that it opeiates on iigiu bouies staiting fiom a
TINKER .xyzcooiuinate file anu the iigiu bouy gioup uefinitions founu in the coiiesponuing .key
file. 0utput is saveu in an upuateu .xyzfile oi in cycle files.

OJ$"&

The N0NTE piogiam implements the Nonte Cailo Ninimization algoiithm uevelopeu by Baiolu
Scheiaga's gioup anu otheis. The pioceuuie takes Nonte Cailo steps foi eithei a single atom oi a
single toisional angle, then peifoims a minimization befoie application of the Netiopolis sampling
methou. This iesults in effective sampling of a mouifieu potential suiface wheie the only possible
eneigy levels aie those of local minima on the oiiginal suiface. The piogiam can be easily mouifieu to
elaboiate on the available move set.

$&<"J$

15 "#$%&' ()*+,) -./0* 15
A tiuncateu Newton minimization methou which iequiies potential eneigy, giauient anu Bessian
infoimation. This pioceuuie has significant auvantages ovei stanuaiu Newton methous, anu is able
to minimize veiy laige stiuctuies completely. Seveial options aie pioviueu with iespect to
minimization methou anu pieconuitioning of the Newton equations. The uefault options aie
iecommenueu unless the usei is familiai with the math involveu. This piogiam opeiates in Caitesian
cooiuinate space anu is faiily toleiant of pooi input stiuctuies. Typical algoiithm iteiation times aie
longei than with nonlineai conjugate giauient oi vaiiable metiic methous, but many fewei iteiations
aie iequiieu foi complete minimization. NEWT0N is usually the best choice foi minimizations to the
u.u1 to u.uuuuu1 kcalmole- level of *+, giauient conveigence. Tests foi uiiections of negative
cuivatuie can be iemoveu, allowing NEWT0N to be useu foi optimization to confoimational
tiansition state stiuctuies (this only woiks if the staiting point is veiy close to the tiansition state).
Input consists of a TINKER .xyzcooiuinates file; output is an upuateu set of minimizeu cooiuinates
anu minimization statistics.

$&<"'J"

The NEWTR0T piogiam is similai to NEWT0N except that it iequiies a .intfile as input anu then
opeiates in teims of uiheuial angles as the minimization vaiiables. Since the uiheuial space Bessian
matiix of an aibitiaiy stiuctuie is often inuefinite, this methou will often not peifoim as well as the
othei, simplei uiheuial angle baseu minimizeis.

JG"#O#S&

The 0PTINIZE piogiam peifoims a optimally conuitioneu vaiiable metiic minimization of an input
stiuctuie ovei Caitesian cooiuinates using an algoiithm uue to William Baviuon. The methou uoes
not peifoim line seaiches, but iequiies computation of eneigies anu giauients as well as stoiage foi
an estimate of the inveise Bessian matiix. The piogiam opeiates on Caitesian cooiuinates fiom a
TINKER .xyzfile. 0PTINIZE will typically conveige somewhat fastei anu moie completely than
NININIZE. Bowevei, the neeu to stoie anu manipulate a full inveise Bessian estimate limits its use to
stiuctuies containing less than a few hunuieu atoms on woikstation class machines. As with the
othei minimizeis, 0PTINIZE neeus input cooiuinates anu an *+, giauient cutoff ciiteiion. The
output cooiuinates aie saveu in upuateu .xyzfiles oi as cycle files.

JG"#'J"

The 0PTIR0T piogiam is similai to 0PTINIZE except that it opeiates on uiheuial angles staiting
fiom a TINKER .intinteinal cooiuinate file. This piogiam is usually the piefeiieu methou foi most
uiheuial angle optimization pioblems since Tiuncateu Newton methous appeai, in oui hanus, to lose
some of theii efficacy in moving fiom Caitesian to toisional cooiuinates.

JG"'#-#I

The 0PTRIuIB piogiam is similai to 0PTINIZE except that it opeiates on iigiu bouies staiting fiom a
TINKER .xyzcooiuinate file anu the iigiu bouy atom gioup uefinitions founu in the coiiesponuing
.keyfile. 0utput is saveu in an upuateu .xyzfile oi in cycle files.

GN"Y

A piogiam that implements a vaiiant of Elbei's Lagiangian multipliei-baseu ieaction path following
algoiithm. The piogiam takes as input a paii of stiuctuial minima as TINKER .xyzfiles, anu then
geneiates a usei specifieu numbei of points along a path thiough confoimational space connecting
the input stiuctuies. The inteimeuiate stiuctuies aie output as TINKER cycle files, anu the highei
16 "#$%&' ()*+,) -./0* 16
eneigy inteimeuiates can be useu as input to a Newton-baseu optimization to locate confoimational
tiansition states.

G88

Implements oui veision of a potential smoothing anu seaich algoiithm foi the global optimization of
moleculai confoimation. An initial stiuctuie in .xyz foimat is fiist minimizeu in Caitesian
cooiuinates on a seiies of incieasingly smootheu potential eneigy suifaces. Then the smoothing
pioceuuie is ieveiseu with minimization on each successive suiface staiting fiom the cooiuinates of
the minimum on the pievious suiface. A local seaich pioceuuie is useu uuiing the backtiacking to
exploie foi alteinative minima bettei than the one founu uuiing the cuiient minimization. The final
iesult is usually a veiy low eneigy confoimation oi, in favoiable cases, the global eneigy minimum
confoimation. The minimum eneigy cooiuinate sets founu on each suiface uuiing both the foiwaiu
smoothing anu backtiacking pioceuuies aie placeu in sequentially numbeieu cycle files.

G88'#-#I

This piogiam implements the potential smoothing anu seaich methou as uesciibeu above foi the PSS
piogiam, but peifoims the computation in teims of keyfile-uefineu iigiu bouy atom gioups insteau of
Caitesian cooiuinates. 0utput is saveu in numbeieu cycle files with the .xyzfile foimat.

G88'J"

This piogiam implements the potential smoothing anu seaich methou as uesciibeu above foi the PSS
piogiam, but peifoims the computation in teims of a set of usei-specifieu uiheuial angles insteau of
Caitesian cooiuinates. 0utput is saveu in numbeieu cycle files with the .intfile foimat.

8NIIP&

A piogiam foi the location of a confoimational tiansition state between two potential eneigy
minima. SABBLE uses a conglomeiation of iueas fiom the Bell-Ciighton quauiatic path anu the
Balgien-Lipscomb synchionous tiansit methous. The basic iuea is to peifoim a nonlineai conjugate
giauient optimization in a subspace oithogonal to a suitably uefineu ieaction cooiuinate. The
piogiam iequiies as input the cooiuinates (TINKER .xyzfiles) of the two minima anu an *+,
giauient conveigence ciiteiion foi the optimization. The cuiient estimate of the tiansition state
stiuctuie is wiitten to the file TSTATE.XYZ. Ciuue tiansition state stiuctuies geneiateu by SABBLE
can sometimes be iefineu using the NEWT0N piogiam. 0ptionally, a scan of the inteiconveision
pathway can be maue at each majoi iteiation.

8?N$

A piogiam foi geneial confoimational seaich of an entiie potential eneigy suiface via a basin
hopping methou. The piogiam takes as input a TINKER .xyz cooiuinates file which is then
minimizeu to finu the fiist local minimum foi a seaich list. A seiies of activations along vaiious
noimal moues fiom this initial minimum aie useu as seeu points foi auuitional minimizations.
Whenevei a pieviously unknown local minimum is locateu it is auueu to the seaich list. When all
minima on the seaich list have been subjecteu to the noimal moue activation without locating
auuitional new minima, the piogiam teiminates. The inuiviuual local minima aie wiitten to cycle
files as they aie uiscoveieu. While the SCAN piogiam can be useu on stanuaiu unuefoimeu potential
eneigy suifaces, we have founu it to be most useful foi quickly ``scanning'' a smootheu eneigy
suiface to enumeiate the majoi basins of attiaction spaning the entiie suiface.

17 "#$%&' ()*+,) -./0* 17
8$#>>&'

A piogiam that implements the Sniffei global optimization algoiithm of Butlei anu Slaminka, a
uisciete veision of uiiewank's global seaich tiajectoiy methou. The piogiam takes an input TINKER
.xyzcooiuinates file anu shakes it vigoiously via a mouifieu uynamics tiajectoiy befoie, hopefully,
settling into a low lying minimum. Some tiial anu eiioi is often iequiieu as the cuiient
implementation is sensitive to vaiious paiameteis anu toleiances that govein the computation. At
piesent, these paiameteis aie not usei accessible, anu must be alteieu in the souice coue. Bowevei,
this methou can uo a goou job of quickly optimizing confoimation within a limiteu iange of
conveigence.

"&8"-'NI

The TESTuRAB piogiam computes anu compaies the analytical anu numeiical fiist ueiivatives (&$!$,
the giauient vectoi) of the potential eneigy foi a Caitesian cooiuinate input stiuctuie. The output
can be useu to test oi uebug the cuiient potential oi any auueu usei uefineu eneigy teims.

"&8"Y&88

The TESTBESS piogiam computes anu compaies the analytical anu numeiical seconu ueiivatives
(&$!$, the Bessian matiix) of the potential eneigy foi a Caitesian cooiuinate input stiuctuie. The
output can be useu to test oi uebug the cuiient potential oi any auueu usei uefineu eneigy teims.

"&8"P#-Y"

A piogiam to compaie the efficiency of uiffeient nonbonueu neighboi methous foi the cuiient
moleculai system. The piogiam times the computation of eneigy anu giauient foi the van uei Waals
anu chaige-chaige electiostatic potential teims using a simple uouble loop ovei all inteiactions anu
using the Nethou of Lights algoiithm to select neighbois. The iesults can be useu to ueciue whethei
the Nethou of Lights has any CP0 time auvantage foi the cuiient stiuctuie. Both methous shoulu give
exactly the same answei in all cases, since the iuentical inuiviuual inteiactions aie computeu by both
methous. The uefault uouble loop methou is fastei when cutoffs aie not useu, oi when the cutoff
spheie contains about half oi moie of the total system of unit cell. In cases wheie the cutoff spheie is
much smallei than the system size, the Nethou of Lights can be much fastei since it avoius
unnecessaiy calculation of uistances beyonu the cutoff iange.

"&8"'J"

The TESTR0T piogiam computes anu compaies the analytical anu numeiical fiist ueiivatives (&$!$,
the giauient vectoi) of the potential eneigy with iespect to uiheuial angles. Input is a TINKER .int
inteinal cooiuinate file. The output can be useu to test oi uebug the cuiient potential functions oi
any auueu usei uefineu eneigy teims.

"#O&'

A simple piogiam to pioviue timing statistics foi eneigy function calls within the TINKER package.
TINER iequiies an input .xyzfile anu outputs the CP0 time (wall clock time on some machine
types) neeueu to peifoim a specifieu numbei of eneigy, giauient anu Bessian evaluations.

"#O&'J"

18 "#$%&' ()*+,) -./0* 18
This piogiam is similai to TINER, only it opeiates ovei uiheuial angles via input of a TINKER .int
inteinal cooiuinate file. In the cuiient veision, the toisional Bessian is computeu numeiically fiom
the analytical toisional giauient.

Z#V'N"&

A piogiam to peifoim vibiational analysis by computing anu uiagonalizing the full Bessian matiix
(&$!$, the seconu paitial ueiivatives) foi an input stiuctuie (a TINKER .xyzfile). Eigenvalues anu
eigenvectois of the mass weighteu Bessian (&$!$, the vibiational fiequencies anu noimal moues) aie
also calculateu. Stiuctuies coiiesponuing to inuiviuual noimal moue motions can be saveu in cycle
files.

Z#V'J"

The piogiam vIBR0T foims the toisional Bessian matiix via numeiical uiffeientiation of the
analytical toisional giauient. The Bessian is then uiagonalizeu anu the eigenvalues aie output. The
piesent veision uoes not compute the kinetic eneigy matiix elements neeueu to conveit the Bessian
into the toisional noimal moues; this will be auueu in a latei veision. The iequiieu input is a TINKER
.intinteinal cooiuinate file.

Q"NP>#"

The XTALFIT piogiam is of use in the automateu fitting of potential paiameteis to ciystal stiuctuie
anu theimouynamic uata. XTALFIT takes as input seveial ciystal stiuctuies (TINKER .xyzfiles with
unit cell paiameteis in coiiesponuing keyfiles) as well as infoimation on lattice eneigies anu uipole
moments of monomeis. The cuiient veision uses a nonlineai least squaies optimization to fit van uei
Waals anu electiostatic paiameteis to the input uata. Bounus can be placeu on the values of the
optimization paiameteis.

Q"NPO#$

A piogiam to peifoim full ciystal minimizations. The piogiam takes as input the stiuctuie
cooiuinates anu unit cell lattice paiameteis. It then alteinates cycles of Newton-style optimization of
the stiuctuie anu conjugate giauient optimization of the ciystal lattice paiameteis. This alteinating
minimization is slowei than moie uiiect optimization of all paiameteis at once, but is somewhat
moie iobust in oui hanus. The symmetiy of the oiiginal ciystal is not enfoiceu, so inteiconveision of
ciystal foims may be obseiveu in some cases.

19 "#$%&' ()*+,) -./0* 19
[2 N00/4/53;B (4/B/4E G+5X+;C) M86+/@4)
This section of the manual contains a biief uesciiption of each of the TINKER stiuctuie manipulation,
geometiic calculation anu auxiliaiy piogiams. A uetaileu example showing how to iun each piogiam
is incluueu in a latei section. The piogiams listeu below aie all pait of the main, suppoiteu
uistiibution. Auuitional souice coue foi vaiious unsuppoiteu piogiams can be founu in the othei
uiiectoiy of the TINKER uistiibution.

N'?Y#Z&

A piogiam foi concatenating TINKER cycle files into a single aichive file; useful foi stoiing the
inteimeuiate iesults of minimizations, uynamics tiajectoiies, anu so on. The aichive file can be
wiitten in TINKER foimat, oi in foimats usable with NSI's InsightII (theii CAR file with 2C)/
extension) oi with XNakemol (theii file foimat with .xmolextension). 0nly active atoms aie wiitten
into the InsightII anu XNakemol output files, allowing uisplay of paitial stiuctuies. The piogiam can
also extiact inuiviuual cycle files fiom a TINKER aichive.

?J''&PN"&

A piogiam to compute time coiielation functions fiom collections of TINKER cycle files. Its use
iequiies a usei supplieu function @+5@*+4E that computes the value of the piopeity foi which a time
coiielation is uesiieu foi two input stiuctuies. A sample ioutine is supplieu that computes eithei a
velocity autocoiielation function oi an *+, stiuctuial supeiposition as a function of time. The main
bouy of the piogiam oiganizes the oveiall computation in an efficient mannei anu outputs the final
time coiielation function.

?'R8"NP

A piogiam foi the manipulation of ciystal stiuctuies incluuing inteiconveision of fiactional anu
Caitesian cooiuinates, geneiation of the unit cell fiom an asymmetiic unit, anu builuing of a
ciystalline block of specifieu size via ieplication of a single unit cell. The piesent veision can hanule
about 2S of the most common space gioups, otheis can easily be auueu as neeueu by mouification of
the ioutine )ECC*4+E.

I#>>(8&

A piogiam to compute the self-uiffusion constant foi a homogeneous liquiu via the Einstein equation.
A pieviously saveu uynamics tiajectoiy is ieau in anu ``unfolueu'' to ieveise tianslation of molecules
uue to use of peiiouic bounuaiy conuitions. The aveiage motion ovei all molecules is then useu to
compute the self-uiffusion constant. While the cuiient piogiam assumes a homogeneous system, it
shoulu be easy to mouify the coue to hanule uiffusion of inuiviuual molecules oi othei uesiieu effects.

I#8"-&JO

A piogiam to peifoim uistance geometiy calculations using vaiiations on the classic metiic matiix
methou. A usei specifieu numbei of stiuctuies consistent with keyfile input uistance anu uiheuial
iestiaints is geneiateu. Bonu length anu angle iestiaints aie ueiiveu fiom the input stiuctuie. Tiial
uistances between the tiiangle smootheu lowei anu uppei bounus can be chosen via any of seveial
metiization methous, incluuing a veiy effective paitial ianuom paiiwise scheme. The coiiect iauius
of gyiation of the stiuctuie is automatically maintaineu by choosing tiial uistances fiom uaussian
uistiibutions of appiopiiate mean anu wiuth. The initial embeuueu stiuctuies can be fuithei iefineu
20 "#$%&' ()*+,) -./0* 20
against a geometiic iestiaint-only potential using eithei a sequential minimization piotocol oi
simulateu annealing.

IJ?(O&$"

The B0C0NENT piogiam is pioviueu as a minimal listing anu uocumentation tool. It opeiates on the
TINKER souice coue, eithei inuiviuual files oi the complete souice listing piouuceu by the commanu
sciipt listing.make, to geneiate lists of ioutines, common blocks oi valiu keywoius. In auuition,
the piogiam has the ability to output a foimatteu paiametei listing fiom the stanuaiu TINKER
paiametei files.

#$"&I#"

A piogiam to allow inteiactive inspection anu alteiation of the inteinal cooiuinate uefinitions anu
values of a TINKER stiuctuie. If the stiuctuie is alteieu, the usei has the option to wiite out a new
inteinal cooiuinates file upon exit.

#$"QRS

A piogiam to conveit a TINKER .intinteinal cooiuinates foimatteu file into a TINKER .xyz
Caitesian cooiuinates foimatteu file.

$(?P&#?

A piogiam foi automateu builuing of nucleic aciu stiuctuies. 0pon inteiactive input of a nucleotiue
sequence with optional phosphate backbone angles, the piogiam builus inteinal anu Caitesian
cooiuinates. Stanuaiu bonu lengths anu angles aie useu. Both BNA anu RNA sequences aie
suppoiteu as aie A-, B- anu Z-foim stiuctuies. Bouble helixes of complementaiy sequence can be
automatically constiucteu via a iigiu uocking of inuiviuual stianus.

GIVQRS

A piogiam foi conveiting a Biookhaven Piotein Bata Bank file (a PBB file) into a TINKER .xyz
Caitesian cooiuinate file. If the PBB file contains only pioteinpeptiue amino aciu iesiuues, then
stanuaiu piotein connectivity is assumeu, anu tiansfeiieu to the 2HE\ file. Foi non-piotein poitions of
the PBB file, atom connectivity is ueteimineu by the piogiam baseu on inteiatomic uistances. The
piogiam also has the ability to auu oi iemove hyuiogen atoms fiom a piotein as iequiieu by the
foice fielu specifieu uuiing the computation.

GJPN'#S&

A piogiam foi computing moleculai polaiizability fiom an atom-baseu uistiibuteu mouel of
polaiizability. A uampeu inteiaction mouel uue to Thole is optionally via keyfile settings. A TINKER
.xyzfile is iequiieu as input. The output consists of the oveiall polaiizability tensoi in the global
cooiuinates anu its eigenvalues.

G'O&I#"

A piogiam foi foimatting anu ienumbeiing TINKER foice fielu paiametei files. When atom types oi
classes aie auueu to a paiametei file, this utility piogiam has the ability to ienumbei all the atom
iecoius sequentially, anu altei type anu class numbeis in all othei paiametei entiies to maintain
consistency.
21 "#$%&' ()*+,) -./0* 21

G'J"&#$

A piogiam foi automateu builuing of peptiue anu piotein stiuctuies. 0pon inteiactive input of an
amino aciu sequence with optional phipsiomegachi angles, BL chiiality, etc., the piogiam builus
inteinal anu Caitesian cooiuinates. Stanuaiu bonu lengths anu angles aie assumeu foi the peptiue.
The piogiam will optionally conveit the stiuctuie to a cyclic peptiue, oi auu eithei oi both N- anu C-
teiminal capping gioups. Atom type numbeis aie automatically assigneu foi the specifieu foice fielu.
The final cooiuinates anu a sequence file aie piouuceu as the output.

'NI#NP

A piogiam to compute the paii iauial uistiibution function between two atom types. The usei
supplies the two atom names foi which the uistiibution function is to be computeu, anu the wiuth of
the uistance bins foi uata analysis. A pieviously saveu uynamics tiajectoiy is ieau as input. The iaw
iauial uistiibution anu a spline smootheu veision aie then output fiom zeio to a uistance equal to
half the minimum peiiouic box uimension. The atom names aie matcheu to the atom name column of
the TINKER 2HE\ file, inuepenuent of atom type.

8GN?&>#PP

A piogiam to compute the volume anu suiface aieas of molecules. 0sing a mouifieu veision of
Connolly's oiiginal analytical uesciiption of the moleculai suiface, the piogiam ueteimines eithei the
van uei Waals, accessible oi moleculai (contactieentiant) volume anu suiface aiea. Both suiface
aiea anu volume aie bioken uown into theii geometiic components, anu suiface aiea is uecomposeu
into the convex contiibution foi each inuiviuual atom. The piobe iauius is input as a usei option, anu
atomic iauii can be set via the keywoiu file. If TINKER aichive files aie useu as input, the piogiam
will compute the volume anu suiface aiea of each stiuctuie in the input file.

8G&?"'(O

A piogiam to compute a powei spectium fiom velocity autocoiielation uata. As input, this piogiam
iequiies a velocity autocoiielation function as piouuceu by the C0RRELATE piogiam. This uata,
along with a usei input time step, aie Fouiiei tiansfoimeu to geneiate the spectial intensities ovei a
wavelength iange. The iesult is a powei spectium, anu the positions of the banus aie those pieuicteu
foi an infiaieu oi Raman spectium. Bowevei, the uata is not weighteu by moleculai uipole moment
ueiivatives as woulu be iequiieu to piouuce coiiect IR intensities.

8(G&'GJ8&

A piogiam to supeiimpose two moleculai stiuctuies in S-uimensions. A vaiiety of options foi input
of the atom sets to be useu uuiing the supeiposition aie piesenteu inteiactively to the usei. The
supeiposition can be mass-weighteu if uesiieu, anu the cooiuinates of the seconu stiuctuie
supeiimposeu on the fiist stiuctuie aie optionally output. If TINKER aichive files aie useu as input,
the piogiam will compute all paiiwise supeipositions between stiuctuies in the input files.

8RVRPQRS

A piogiam foi conveiting a TRIP0S Sybyl N0L2 file into a TINKER .xyzCaitesian cooiuinate file.
The cuiient veision of the piogiam uoes not attempt to conveit the Sybyl atoms types into the active
TINKER foice fielu types, &$!$, all atoms types aie simply set to zeio.

22 "#$%&' ()*+,) -./0* 22
QRS&I#"

A piogiam that peifoims anu of a vaiiety of manipulations on an input TINKER .xyz Caitesian
cooiuinates foimatteu file. The piesent veision of the piogiam has the following inteiactively
selectable options: (1) 0ffset the Numbeis of the Cuiient Atoms, (2) Beletion of Inuiviuual Specifieu
Atoms, (S) Beletion of Specifieu Types of Atoms, (4) Beletion of Atoms outsiue Cutoff Range, (S)
Inseition of Inuiviuual Specifieu Atoms, (6) Replace 0lu Atom Type with a New Type, (7) Assign
Connectivities baseu on Bistance, (8) Conveit 0nits fiom Bohis to Angstioms, (9) Inveit thiu 0iigin
to give Niiioi Image, (1u) Tianslate Centei of Nass to the 0iigin, (11) Tianslate a Specifieu Atom to
the 0iigin, (12) Tianslate anu Rotate to Ineitial Fiame, (1S) Nove to Specifieu Rigiu Bouy
Cooiuinates, (14) Cieate anu Fill a Peiiouic Bounuaiy Box, (1S) Soak Cuiient Nolecule in Box of
Solvent, (16) Appenu anothei XYZ file to Cuiient 0ne. In most cases, multiply options can be applieu
sequentially to an input file. At the enu of the euiting piocess, a new veision of the oiiginal .xyzfile
is wiitten as output.

QRS#$"

A piogiam foi conveiting a TINKER .xyzCaitesian cooiuinate foimatteu file into a TINKER .int
inteinal cooiuinates foimatteu file. This piogiam can optionally use an existing inteinal cooiuinates
file as a template foi the connectivity infoimation.

QRSGIV

A piogiam foi conveiting a TINKER .xyzCaitesian cooiuinate file into a Biookhaven Piotein Bata
Bank file (a PBB file).

QRS8RVRP

A piogiam to conveit a TINKER .xyzCaitesian cooiuinates file into a TRIP0S Sybyl N0L2 file. The
conveision geneiates only the N0LEC0LE, AT0N, B0NB anu S0BSTR0CT0RE iecoiu type in the
N0L2 file. ueneiic Sybyl atom types aie useu in most cases; while these atom types may neeu to be
alteieu in some cases, Sybyl is usually able to coiiectly uisplay the iesulting N0L2 file.

23 "#$%&' ()*+,) -./0* 23
]2 8@*6/;B >*;4.+*) MO*4750)
This section contains seveial shoit notes with fuithei infoimation about TINKER methouology,
algoiithms anu special featuies. The uiscussion is not intenueu to be exhaustive, but iathei to explain
featuies anu capabilities so that useis can make moie complete use of the package.

>/B* Z*+)/53 $.CA*+)

All of the input anu output file types ioutinely useu by the TINKER package aie capable of existing as
multiple veisions of a base file name. Foi example, if the piogiam XYZINT is iun on the input file
molecule.xyz, the output inteinal cooiuinates file will be wiitten to molecule.int. If a file
nameu molecule.intis alieauy piesent piioi to iunning XYZINT, then the output will be wiitten
insteau to the next available veision, in this case to molecule.int_2. In fact the output is geneially
wiitten to the lowest available, pieviously unuseu veision numbei (molecule.int_3,
molecule.int_4, !"#., as high as neeueu). Input file names aie hanuleu similaily. If simply
moleculeoi molecule.xyzis enteieu as the input file name upon iunning XYZINT, then the
highest veision of molecule.xyzwill be useu as the actual input file. If an explicit veision numbei
is enteieu as pait of the input file name, then the specifieu veision will be useu as the input file.

The veision numbei scheme will be iecognizeu by many oluei useis as a holuovei fiom the vNS
oiigins of the fiist veision of the TINKER softwaie. It has been maintaineu to make it easiei to chain
togethei multiple calculations that may cieate seveial new veisions of a given file, anu to make it
moie uifficult to acciuently oveiwiite a neeueu iesult. The veision scheme applies to most uses of
many common TINKER file types such as .xyz, .int, .key, .arc. It is not useu when an
oveiwiitten file ``upuate'' is obviously the coiiect action, foi example, the .dynmoleculai uynamics
iestait files. Foi those useis who piefei a moie 0nix-like opeiation, anu uo not uesiie use of file
veisions, this featuie can be tuineu off by auuing the N0vERSI0N keywoiu to the applicable TINKER
keyfile.

The veision scheme as implementeu in TINKER uoes have two known quiiks. Fiist, it becomes
impossible to uiiectly use the oiiginal unveisioneu copy of a file if highei veision numbeis aie
piesent. Foi example, if the files molecule.xyz anu molecule.xyz_2 both exist, then
molecule.xyzcannot be accesseu as input by XYZINT. If molecule.xyzis enteieu in iesponse to
the input file name question, molecule.xyz_2(oi the highest piesent veision numbei) will be
useu as input. The only woikaiounu is to copy oi iename molecule.xyzto something else, say
molecule.new, anu use that name foi the input file. Seconuly, missing veision numbeis always enu
the seaich foi the highest available veision numbei; &$!$, veision numbeis aie assumeu to be
consecutive anu without gaps. Foi example, if molecule.xyz, molecule.xyz_2 anu
molecule.xyz_4aie piesent, but not molecule.xyz_3, then molecule.xyz_2will be useu as
input to XYZINT if moleculeis given as the input file name. Similaily, output files will fill in gaps in
an alieauy existing set of file veisions.

?5CC;30 P/3* J@4/53)

Nany opeiating systems oi compilei supplieu-libiaiies make available something like the stanuaiu
0nix iaigc anu getaig ioutines foi captuiing commanu line aiguments. 0n these machines most of
the TINKER piogiams suppoit a selection of commanu line aiguments anu options. The name of the
keyfile to be useu foi a calculation is ieau fiom the aigument following a -k(equivalent to eithei -
keyoi -keyfile, case insensitive) commanu line aigument. Note that the -koptions can appeai
anywheie on the commanu line following the executable name. All othei commanu line aiguments,
excepting the name of the executable piogiam itself, aie tieateu as input aiguments. These input
24 "#$%&' ()*+,) -./0* 24
aiguments aie ieau fiom left to iight anu inteipieteu in oiuei as the answeis to questions that woulu
be askeu by an inteiactive invocation of the same TINKER piogiam. Foi example, the following
commanu line:

newton molecule -k test a a 0.01

will invoke the NEWT0N piogiam on the stiuctuie file molecule.xyzusing the keyfile test.key,
automatic moue [a]foi both the methou anu pieconuitioning, anu 0.01foi the RNS giauient pei
atom teimination ciiteiion in kcalmole-. Pioviueu that the foice fielu paiametei set, !"#. is
pioviueu in test.key, the above compuation will pioceue uiiectly fiom the commanu line
invocation without fuithei inteiactive input.

()* 53 O/6+5)594 </305:) 8E)4*C)

TINKER executables foi Niciosoft PC systems shoulu be iun fiom the B0S oi Commanu Piompt
winuow available unuei the vaiious veisions of Winuows. The TINKER executable uiiectoiy shoulu
be auueu to youi path via the autoexec.bat file oi similai. If using Win2uuu oi XP, set the numbei of
sciollable lines in the Commanu Piompt winuow to a veiy laige numbei, so that you will be able to
inspect scieen output aftei it flies by. With Win9S98, these Commanu Piompt winuows aie only
able to scioll a small numbei of lines ((+(-&./0), so TINKER piogiams which geneiate laige amounts
of scieen output shoulu be iun such that output will be ieuiiecteu to a file. This can be accomplisheu
by iunning the TINKER piogiam in batch moue oi by using the 0nix-like output ieuiiection builu
into B0S. Foi example, the commanu:

dynamic < molecule.inp > molecule.log

will iun the TINKER uynamic piogiam taking input fiom the file molecule.inpanu senuing output
to molecule.log. Also note that commanu line options as uesciibeu above aie available with the
uistiibuteu TINKER executables.

Anothei alteinative, paiticulaily attiactive to those alieauy familiai with Linux oi 0nix systems, is to
uownloau the Cygwin package cuiiently available unuei uPL license fiom the site
http://source.redhat.com/cygwin/. The cygwin tools pioviue many of the uN0 tools,
incluuing a bash shell winuow fiom which TINKER piogiams can be iun.

If the uistiibuteu TINKER executables aie iun uiiectly fiom Winuows by uouble clicking on the
piogiam icon, then the piogiam will iun in its own winuow. Bowevei, upon completion of the
piogiam the winuow will close anu scieen output will be lost. Any output files wiitten by the
piogiam will, of couise, still be available. The Winuows behavioi can be changeu by auuing the EXIT-
PA0SE keywoiu to the keyfile. This keywoiu causes the executation winuow to iemain open aftei
completion until the ``Entei'' key is piesseu.

()* 53 N@@B* O;6/345)7 8E)4*C)

The TINKER executables aie best iun unuei Nac 0S X in a ``teiminal'' application winuow wheie
behavioi is iuentical to that in a Linux teiminal. At piesent the Foice Fielu Exploiei u0I foi TINKER
will not iun on 0S X since the iequiieu }avaSB extensions aie unavailable.

We have uiscontinueu active suppoit foi Nac 0S 9. Bowevei, the 0S 9 veisions of TINKER aie iun by
uouble clicking on a piogiam icon. The piogiam will iun in its own winuow to which all ``scieen''
output will be uiiecteu. 0pon piogiam teimination the winuow will iemain active penuing a final
ietuin enteieu by the usei which will close the winuow. Piioi to the final ietuin, the contents of the
scieen winuow can be saveu to a file via the clipboaiu foi peimanent stoiage. Note that Nacintosh
25 "#$%&' ()*+,) -./0* 25
0S9 uses a colon insteau of a foiwaiu- oi back-slash as the uiiectoiy sepaiatoi, so keyfiles tiansfeieu
fiom othei machines will neeu to be alteieu accoiuingly.

N45C"E@*) !"2 N45C?B;))*)

Nanipulation of atom types anu the piolifeiation of paiameteis as atoms aie fuithei subuiviueu into
new types is the bane of foice fielu calculation. Foi example, if each topologically uistinct atom
aiising fiom the 2u natuial amino acius is given a uiffeient atom type, then about Suu sepaiate type
aie iequiieu (this ignoies the uiffeient N- anu C-teiminal foims of the iesiuues, uiasteieotopic
hyuiogens, !"#.). Bowevei, all these types leau to liteially thousanus of uiffeient foice fielu
paiameteis. In fact, theie aie many thousanus of uistinct toisional paiameteis alone. It is impossible
at piesent to fully optimize each of these paiameteis; anu even if we coulu, a gieat many of the
paiameteis woulu be neaily iuentical. Two somewhat complimentaiy solutions aie available to
hanule the piolifeiation of paiameteis. The fiist is to specify the moleculai fiagments to which a
given paiametei can be applieu in teims of a chemical stiuctuie language, SNILES stiings foi
example. Some commeicial systems, such as the TRIP0S Sybyl softwaie, make use of such a scheme
to paise stiuctuies anu assign foice fielu paiameteis.

A seconu geneial appioach is to use hieiaichical cascaues of paiametei gioups. TINKER uses a
simple veision of this scheme. Each TINKER foice fielu atom has both an atom "12! numbei anu an
atom #)(,, numbei. The types aie subsets of the atom classes, &$!$, seveial uiffeient atom types can
belong to the same atom class. Foice fielu paiameteis that aie somewhat less sensitive to local
enviionment, such as local geometiy teims, aie then pioviueu anu assigneu baseu on atom class.
0thei eneigy paiameteis, such as electiostatic paiameteis, that aie veiy enviionment uepenuent aie
assigneu ovei the atom types. This gieatly ieuuces the numbei of inuepenuent multiple-atom
paiameteis like the foui-atom toisional paiameteis.

?;B6.B;4/53) 53 G;+4/;B 84+.64.+*)

Two methous aie available foi peifoiming eneigetic calculations on poitions oi substiuctuies within
a full moleculai system. TINKER allows uivision of the entiie system into (#"&3! anu &.(#"&3! paits
which can be uefineu via keywoius. In subsequent calculations, such as minimization oi uynamics,
only the active poitions of the system aie alloweu to move. The foice fielu engine iesponus to the
activeinactive uivision by computing all eneigetic inteiactions involving at least one active atom; &$!$,
any inteiaction whose eneigy can change with the motion of one oi moie active atoms is computeu.

The seconu methou foi paitial stiuctuie computation involves uiviuing the oiiginal system into a set
of atom /*452,. As befoie, the gioups can be specifieu via appiopiiate keywoius. The cuiient TINKER
implementation allows specification of up to a maximum numbei of gioups as given in the sizes.i
uimensioning file. The gioups must be uisjoint in that no atom can belong to moie than one gioup.
Fuithei keywoius allow the usei to specify which intia- anu inteigioup sets of eneigetic inteiactions
will contiibute to the total foice fielu eneigy. Weights foi each set of inteiactions in the total eneigy
can also be input. A specific eneigetic inteiaction is assigneu to a paiticulai intia- oi inteigioup set if
all the atoms involveu in the inteiaction belong to the gioup (intia-) oi paii of gioups (intei-).
Inteiactions involving atoms fiom moie than two gioups aie not computeu.

Note that the gioups methou anu activeinactive methou use uiffeient assignment pioceuuies foi
inuiviuual inteiactions. The activeinactive scheme is intenueu foi situations wheie only a poition of
a system is alloweu to move, but the total eneigy neeus to ieflect the piesence of the iemaining
inactive poition of the stiuctuie. The gioups methou is intenueu foi use in iigiu bouy calculations,
anu is neeueu foi ceitain kinus of fiee eneigy peituibation calculations.

O*4;B ?5C@B*H*) ;30 YE@*+^;B*34 8@*6/*)
26 "#$%&' ()*+,) -./0* 26

The uistiibution veision of TINKER comes uimensioneu foi a maximum atomic cooiuination numbei
of foui as neeueu foi stanuaiu oiganic compounus. In oiuei to use TINKER foi calculations on
species containing highei cooiuination numbeis, simply change the value of the paiametei maxval
in the mastei uimensioning file sizes.ianu iebuilt the package. Note that this paiametei value
shoulu not be set laigei than necessaiy since laige values can slow the execution of poitions of some
TINKER piogiams.

Nany moleculai mechanics appioaches to inoiganic anu metal stiuctuies use an angle benuing teim
which is softei than the usual haimonic benuing potential. TINKER implements a Fouiiei benuing
teim similai to that useu by the Lanuis gioup's SBAPES foice fielu. The paiameteis foi specific
Fouiiei angle teims aie supplieu via the ANuLEF paiametei anu keywoiu foimat. Note that a Fouiiei
teim will only be useu foi a paiticulai angle if a coiiesponuing haimonic angle teim is not piesent in
the paiametei file.

We aie now collaboiating with Anueis Cailsson's gioup in St. Louis to auu his tiansition metal liganu
fielu teim to TINKER. Suppoit foi this auuitional potential functional foim is alieauy in the TINKER
souice coue, anu we plan to ielease the eneigy ioutines aftei fuithei testing anu paiameteiization.

$*/X7A5+ O*4750) 95+ $53A530*0 "*+C)

In auuition to stanuaiu uouble loop methous, the Nethou of Lights is available to speeu neighboi
seaiching. This methou baseu on taking inteisections of soiteu atom lists can be much fastei foi
pioblems wheie the cutoff uistance is significantly smallei than half the maximal cell uimension. The
cuiient veision of TINKER uoes not implement the ``neighboi list'' schemes common to many othei
simulation packages.

G*+/50/6 V5.30;+E ?530/4/53)

Both spheiical cutoff images oi ieplicates of a cell aie suppoiteu by all TINKER piogiams that
implement peiiouic bounuaiy conuitions. Whenevei the cutoff uistance is too laige foi the minimum
image to be the only ielevant neighboi (&$!$, half the minimum box uimension foi oithogonal cells),
TINKER will automatically switch fiom the image foimalism to use of ieplicateu cells.

I/)4;36* ?.4599) 95+ &3*+XE >.364/53)

Polynomial eneigy switching ovei a winuow is useu foi teims whose eneigy is small neai the cutoff
uistance. Foi monopole electiostatic inteiactions, which aie quite laige in typical cutoff ianges, a two
polynomial multiplicative-auuitive shifteu eneigy switch unique to TINKER is applieu. The TINKER
methou is similai in spiiit to the foice switching methous of Steinbach anu Biooks, 6$ 74+25"$ 78!+$,
#$, 667-68S (1994). While the paiticle mesh Ewalu methou is piefeiieu when peiiouic bounuaiy
conuitions aie piesent, TINKER's shifteu eneigy switch with ieasonable switching winuows is quite
satisfactoiy foi most ioutine moueling pioblems. The shifteu eneigy switch minimizes the
peituibation of the eneigy anu the giauient at the cutoff to acceptable levels. Pioblems shoulu aiise
only if the piopeity you wish to monitoi is known to iequiie explicit inclusion of long iange
components (&$!$, calculation of the uielectiic constant, !"#.).

&:;B0 8.CC;4/53) O*4750)

TINKER contains a veisions of the Ewalu summation technique foi inclusion of long iange
electiostatic inteiactions via peiiouic bounuaiies. The paiticle mesh Ewalu (PNE) methou is
available foi simple chaige-chaige potentials, while iegulai Ewalu is pioviueu foi polaiizable atomic
multipole inteiactions. The accuiacy anu speeu of the iegulai anu PNE calculations is uepenuent on
27 "#$%&' ()*+,) -./0* 27
seveial inteiielateu paiameteis. Foi both methous, the Ewalu coefficient anu ieal-space cutoff
uistance must be set to ieasonable anu complementaiy values. Auuitional contiol vaiiables foi
iegulai Ewalu aie the fiactional coveiage anu numbei of vectois useu in iecipiocal space. Foi PNE
the auuitional contiol values aie the B-spline oiuei anu chaige giiu uimensions. Complete contiol
ovei all of these paiameteis is available via the TINKER keyfile mechanism. By uefault TINKER will
select a set of paiameteis which pioviue a ieasonable compiomise between accuiacy anu speeu, but
these shoulu be checkeu anu mouifieu as necessaiy foi each inuiviuual system.

?534/3..C85B^;4/53 O50*B)

Seveial alteinative continuum solvation algoiithms aie containeu within TINKER. All of these aie
accesseu via the S0LvATE keywoiu anu its mouifieis. Two simple suiface aiea methous aie
implementeu: the ASP methou of Eisenbeig anu NcLachlan, anu the SASA methou fiom Scheiaga's
gioup. These methous aie applicable to any of the stanuaiu TINKER foice fielus. vaiious schemes
baseu on the geneializeu Boin foimalism aie also available: the oiiginal 199u numeiical ``0nion-
shell'' uBSA methou fiom Still's gioup, the 1997 analytical uBSA methou also uue to Still, a
paiiwise uescieening algoiithm oiiginally pioposeu by Bawkins, Ciamei anu Tiuhlai, anu the
analytical continuum solvation (ACE) methou of Schaefei anu Kaiplus. At piesent, the geneializeu
Boin methous shoulu only be useu with foice fielus having simple paitial chaige electiostatic
inteiactions.

Some fuithei comments aie in oiuei iegaiuing the uBSA-style solvation mouels. The ``0nion-shell''
mouel is pioviueu mostly foi compaiison puiposes. It uses an exact, analytical suiface aiea
calculation foi the cavity teim anu the numeiical scheme uesciibeu in the oiiginal papei foi the
polaiization teim. This methou is veiy slow, especially foi laige systems, anu uoes not contain the
contiibution of the Boin iauii chain iule teim to the fiist ueiivatives. We iecommenu its use only foi
single-point eneigy calculations. The othei uBSA methous (``analytical'' Still, B-C-T paiiwise
uescieening, anu ACE) use an appioximate cavity teim baseu on Boin iauii, anu uo contain fully
coiiect ueiivatives incluuing the Boin iauii chain iule contiibution. These methous all scale in CP0
time with the squaie of the size of the system, anu can be useu with minimization, moleculai
uynamics anu laige molecules.

Finally, we note that the ACE solvation mouel shoulu not be useu with the cuiient veision of TINKER.
The algoiithm is fully implementeu in the souice coue, but paiameteiization is not complete. As of
late 2uuu, paiametei values aie only available in the liteiatuie foi use of ACE with the oluei
CBARNN19 foice fielu. We plan to uevelop values foi use with moie mouein all-atom foice fielus,
anu these will be incoipoiateu into TINKER sometime in the futuie.

G5B;+/\;AB* O.B4/@5B* &B*64+5)4;4/6)

Atomic multipole electiostatics thiough the quauiupole moment is suppoiteu by the cuiient veision
of TINKER, as is eithei mutual oi uiiect uipole polaiization. Ewalu summation is available foi
inclusion of long iange inteiactions. Calculations aie implementeu via a mixtuie of the CCPS
algoiithms of W. Smith anu the Applequist-Bykstia Caitesian polytensoi methou. At piesent
analytical eneigy anu Caitesian giauient coue is pioviueu.

The TINKER package allows intiamoleculai polaiization to be tieateu via a veision of the inteiaction
uamping scheme of Thole. To implement the Thole scheme, it is necessaiy to set all the mutual-1x-
scalekeywoius to a value of one. The othei polaiization scaling keywoiu seiies, direct-1x-
scaleanu polar-1x-scale, can be set inuepenuently to enable a wiue vaiiety of polaiization
mouels. In oiuei to use an Applequist-style mouel without polaiization uamping, simply set the
polar-dampkeywoiu to zeio.

28 "#$%&' ()*+,) -./0* 28
G54*34/;B &3*+XE 8C5547/3X

veisions of oui Potential Smoothing anu Seaich (PSS) methouology have been implementeu within
TINKER. This methous belong to the same geneial family as Scheiaga's Biffusion Equation Nethou,
Stiaub's uaussian Bensity Annealing, Shalloway's Packet Annealing anu veischelue's Effective
Biffuseu Potential, but oui algoiithms ieflect oui own ongoing ieseaich in this aiea. In many ways
the TINKER potential smoothing methous aie the ueteiministic analog of stochastic simulateu
annealing. The PSS algoiithms aie veiy poweiful, but aie ielatively new anu aie still unueigoing
mouification, testing anu calibiation within oui ieseaich gioup. This veision of TINKER also incluues
a basin-hopping confoimational scanning algoiithm in the piogiam SCAN which is paiticulaily
effective on smootheu potential suifaces.

I/)4;36* -*5C*4+E O*4+/\;4/53

A much impioveu anu veiy fast ianuom paiiwise metiization scheme is available which allows goou
sampling uuiing tiial uistance matiix geneiation without the usual stiuctuial anomalies anu CP0
constiaints of othei metiization pioceuuies. An outline of the methouology anu its application to
NNR N0E-baseu stiuctuie iefinement is uesciibeu in the papei by Bousuon, !" (). in 6$ 94)$ :&4)$, %&',
S8S-6u2 (1996). We have obtaineu goou iesults with something like the keywoiu phiase trial-
distribution pairwise 5, which peifoims S% paitial ianuom paiiwise metiization. Foi
stiuctuies ovei seveial hunuieu atoms, a value less than S foi the peicentage of metiization shoulu
be fine.

29 "#$%&' ()*+,) -./0* 29
_2 ()* 59 47* %*E:5+0 ?534+5B >/B*
()/3X %*E:5+0) 45 ?534+5B "#$%&' ?;B6.B;4/53)
This section contains a uesciiption of the ovei Suu keywoiu paiameteis which may be useu to uefine
oi altei the couise of a TINKER calculation. The keywoiu contiol file is optional in the sense that all
of the TINKER piogiams will iun in the absence of a keyfile anu will simply use uefault values oi
queiy the usei foi neeueu infoimation. Bowevei, the keywoius allow use of a wiue vaiiety of
algoiithmic anu pioceuuial options, many of which aie unavailable inteiactively.

Keywoius aie ieau fiom the keywoiu contiol file. All piogiams look fiist foi a keyfile with the same
base name as the input moleculai system anu enuing in the extension .key. If this file uoes not exist,
then TINKER tiies to use a geneiic keyfile with the name tinker.keyanu locateu in the same
uiiectoiy as the input system. If neithei a system-specific noi a geneiic keyfile is piesent, TINKER
will continue by using uefault values foi keywoiu options anu asking inteiactive questions as
necessaiy.

TINKER seaiches the keyfile uuiing the couise of a calculation foi ielevant keywoius that may be
piesent. All keywoius must appeai as the fiist woiu on the line. Any blank space to the left of the
keywoiu is ignoieu, anu all contents of the keyfiles aie case insensitive. Some keywoius take
mouifieis; &$!$, TINKER looks fuithei on the same line foi auuitional infoimation, such as the value of
some paiametei ielateu to the keywoiu. Nouifiei infoimation is ieau in fiee foimat, but must be
completely containeu on the same line as the oiiginal keywoiu. Any lines containeu in the keyfile
which uo not qualify as valiu keywoiu lines aie tieateu as comments anu aie simply ignoieu.

Seveial keywoius take a list of integei values (atom numbeis, foi example) as mouifieis. Foi these
keywoius the integeis can simply be listeu explicitly anu sepaiateu by spaces, commas oi tabs. If a
iange of numbeis is uesiieu, it can be specifieu by listing the negative of the fiist numbei of the
iange, followeu by a sepaiatoi anu the last numbei of the iange. Foi example, the keywoiu line
ACTIVE 4 -9 17 23coulu be useu to auu atoms 4, 9 thiough 17, anu 2S to the set of active atoms
uuiing a TINKER calculation.

%*E:5+0) -+5.@*0 AE >.364/53;B/4E

Listeu below aie the available TINKER keywoius soiteu into gioups by geneial function. The section
enus with an alphabetical list containing each inuiviuual keywoiu, along with a biief uesciiption of its
action, possible keywoiu mouifieis, anu usage examples.

J("G(" ?J$"'JP %&R<J'I8

ARCBIvE BEB0u BIuITS
ECB0 EXIT-PA0SE N0vERSI0N
0vERWRITE PRINT00T SAvE-CYCLE
SAvE-F0RCE SAvE-INB0CEB SAvE-vEL0CITY
vERB0SE WRITE00T

>J'?& >#&PI 8&P&?"#J$ %&R<J'I8

F0RCEFIELB PARANETERS

GJ"&$"#NP >($?"#J$ 8&P&?"#J$ %&R<J'I8

30 "#$%&' ()*+,) -./0* 30
ANuANuTERN ANuLETERN B0NBTERN
CBARuETERN CBuBPLTERN BIP0LETERN
EXTRATERN INPR0PTERN INPT0RSTERN
NETALTERN NP0LETERN 0PBENBTERN
0PBISTTERN PIT0RSTERN P0LARIZETERN
RESTRAINTERN RXNFIELBTERN S0LvATETERN
STRBNBTERN STRT0RTERN T0RSI0NTERN
T0RT0RTERN 0REYTERN vBWTERN

GJ"&$"#NP >($?"#J$ GN'NO&"&' %&R<J'I8

ANuANu ANuLE ANuLES
ANuLE4 ANuLES ANuLEF
AT0N BI0TYPE B0NB
B0NBS B0NB4 B0NBS
CBARuE BIP0LE BIP0LES
BIP0LE4 BIP0LES ELECTNEu
BB0NB INPR0PER INPT0RS
NETAL N0LTIP0LE 0PBENB
0PBIST PIAT0N PIB0NB
PIT0RS P0LARIZE S0LvATE
STRBNB STRT0RS T0RSI0N
T0RSI0N4 T0RSI0NS T0RT0R
0REYBRAB vBW vBW14
vBWPR

&$&'-R ($#" ?J$Z&'8#J$ %&R<J'I8

ANuLE0NIT ANuANu0NIT B0NB0NIT
ELECTRIC INPR0P0NIT INPT0R0NIT
0PBENB0NIT 0PBIST0NIT PIT0RS0NIT
STRBNB0NIT STRT0R0NIT T0RSI0N0NIT
T0RT0R0NIT 0REY0NIT

PJ?NP -&JO&"'R >($?"#J$NP >J'O %&R<J'I8

ANuLE-C0BIC ANuLE-Q0ARTIC ANuLE-PENTIC
ANuLE-SEXTIC B0NB-C0BIC B0NB-Q0ARTIC
B0NBTYPE NN2-STRBNB PISYSTEN
0REY-C0BIC 0REY-Q0ARTIC

ZN$ I&' <NNP8 >($?"#J$NP >J'O %&R<J'I8

A-EXPTERN B-EXPTERN C-EXPTERN
BELTA-BALuREN EPSIL0NR0LE uANNA-BALuREN
uA0SSTYPE RABI0SR0LE RABI0SSIZE
RABI0STYPE vBW-12-SCALE vBW-1S-SCALE
vBW-14-SCALE vBW-1S-SCALE vBW-C0RRECTI0N
vBWINBEX vBWTYPE

&P&?"'J8"N"#?8 >($?"#J$NP >J'O%&R<J'I8

CBu-12-SCALE CBu-1S-SCALE CBu-14-SCALE
31 "#$%&' ()*+,) -./0* 31
CBu-1S-SCALE CBu-B0FFER BIELECTRIC
BIRECT-11-SCALE BIRECT-12-SCALE BIRECT-1S-SCALE
BIRECT-14-SCALE NP0LE-12-SCALE NP0LE-1S-SCALE
NP0LE-14-SCALE NP0LE-1S-SCALE N0T0AL-11-SCALE
N0T0AL-12-SCALE N0T0AL-1S-SCALE N0T0AL-14-SCALE
P0LAR-12-SCALE P0LAR-1S-SCALE P0LAR-14-SCALE
P0LAR-1S-SCALE P0LAR-ASPC P0LAR-EPS
P0LAR-S0R P0LARIZATI0N REACTI0NFIELB

$J$VJ$I&I ?("J>> %&R<J'I8

CBu-C0T0FF CBu-TAPER C0T0FF
BPL-C0T0FF BPL-TAPER BESS-C0T0FF
LIuBTS NP0LE-C0T0FF NP0LE-TAPER
NEIuBB0R-uR00PS NE0TRAL-uR00PS P0LYNER-C0T0FF
TAPER TR0NCATE vBW-C0T0FF
vBW-TAPER

&<NPI 8(OON"#J$ %&R<J'I8

EWALB EWALB-ALPBA EWALB-B00NBARY
EWALB-C0T0FF PNE-uRIB PNE-0RBER

?'R8"NP PN""#?& M G&'#JI#? VJ($IN'R %&R<J'I8

A-AXIS B-AXIS C-AXIS
ALPBA BETA uANNA
N0-SYNNETRY 0CTABEBR0N SPACEuR00P
X-AXIS Y-AXIS Z-AXIS

$&#-YVJ' P#8" %&R<J'I8

CBu-LIST LIST-B0FFER NP0LE-LIST
NEIuBB0R-LIST vBW-LIST

JG"#O#SN"#J$ %&R<J'I8

ANuNAX CAPPA FCTNIN
Bu0ESS INTNAX LBFuS-vECT0RS
NAXITER NEWBESS NEXTITER
SL0PENAX STEEPEST-BESCENT STEPNAX
STEPNIN

OJP&?(PN' IR$NO#?8 %&R<J'I8

BEENAN-NIXINu BEuREES-FREEB0N INTEuRAT0R
REN0vE-INERTIA

"Y&'OJ8"N" M VN'J8"N" %&R<J'I8

ANIS0-PRESS0RE BAR0STAT C0LLISI0N
C0NPRESS FRICTI0N FRICTI0N-SCALINu
TA0-PRESS0RE TA0-TENPERAT0RE TBERN0STAT
32 "#$%&' ()*+,) -./0* 32
v0L0NE-N0vE v0L0NE-SCALE v0L0NE-TRIAL

"'N$8#"#J$ 8"N"& %&R<J'I8

BIvERuE uANNANIN REB0CE
SABBLEP0INT

I#8"N$?& -&JO&"'R %&R<J'I8

TRIAL-BISTANCE TRIAL-BISTRIB0TI0N

Z#V'N"#J$NP N$NPR8#8 %&R<J'I8

IB0NP vIB-R00TS vIB-T0LERANCE

#OGP#?#" 8JPZN"#J$ %&R<J'I8

B0RN-RABI0S uK-RABI0S uKC
uKR S0LvENT-PRESS0RE S0RFACE-TENSI0N

GJ#88J$`VJP"SON$$ %&R<J'I8

AuRIB APBS-uRIB BCFL
CuCENT CuRIB FuCENT
FuRIB I0N Nu-A0T0
Nu-NAN0AL PB-RABI0S PBIE
SBENS SBIE SNIN
SRAB SRFN SWIN

ON"Y&ON"#?NP NP-J'#"YO %&R<J'I8

FFT-PACKAuE RANB0NSEEB

GN'NPP&P#SN"#J$ %&R<J'I8

0PENNP-TBREABS

>'&& &$&'-R G&'"('VN"#J$ %&R<J'I8

CBu-LANBBA BPL-LANBBA LANBBA
LIuANB NP0LE-LANBBA N0TATE
P0LAR-LANBBA vBW-LANBBA

GN'"#NP 8"'(?"('& %&R<J'I8

ACTIvE uR00P uR00P-INTER
uR00P-INTRA uR00P-N0LEC0LE uR00P-SELECT
INACTIvE

?J$8"'N#$" M '&8"'N#$" %&R<J'I8

BASIN ENF0RCE-CBIRALITY RATTLE
RATTLE-BISTANCE RATTLE-EPS RATTLE-LINE
RATTLE-0RIuIN RATTLE-PLANE RESTRAIN-ANuLE
33 "#$%&' ()*+,) -./0* 33
RESTRAIN-BISTANCE RESTRAIN-uR00PS RESTRAIN-P0SITI0N
RESTRAIN-T0RSI0N SPBERE WALL

GN'NO&"&' >#""#$- %&R<J'I8

FIT-ANuLE FIT-B0NB FIT-0PBENB
FIT-STRBNB FIT-T0RSI0N FIT-0REY
FIX-ANuLE FIX-B0NB FIX-BIP0LE
FIX-N0N0P0LE FIX-0PBENB FIX-Q0ABR0P0LE
FIX-STRBNB FIX-T0RSI0N FIX-0REY
P0TENTIAL-AT0NS P0TENTIAL-FIT P0TENTIAL-0FFSET
P0TENTIAL-SBELLS P0TENTIAL-SPACINu TARuET-BIP0LE
TARuET-Q0ABR0P0LE

GJ"&$"#NP 8OJJ"Y#$- %&R<J'I8

BEF0RN BIFF0SE-CBARuE BIFF0SE-T0RSI0N
BIFF0SE-vBW SN00TBINu

I*)6+/@4/53 59 #30/^/0.;B %*E:5+0)

The following is an alphabetical list of the TINKER keywoius along with a biief uesciiption of the
action of each keywoiu anu iequiieu oi optional paiameteis that can be useu to extenu oi mouify
each keywoiu. The foimat of possible mouifieis, if any, is shown in biackets following each keywoiu.

N`NQ#8 a+*;Bb Sets the value of the a-axis length foi a ciystal unit cell, oi, equivalently, the X-axis
length foi a peiiouic box. The length value in Angstioms is listeu aftei the keywoiu.

N`&QG"&'O a+*;Bb Sets the value of the ``A'' piemultipliei teim in the Buckingham van uei Waals
function, &$!$, the value of A in the foimula E
vuw
= ! { A exp|-B(R
o
R)j - C (R
o
R)
6
}.

N?"#Z& a/34*X*+ B/)4b Sets the list of active atoms uuiing a TINKER computation. Inuiviuual
potential eneigy teims aie computeu when at least one atom involveu in the teim is active. Foi
Caitesian space calculations, active atoms aie those alloweu to move. Foi toisional space
calculations, iotations aie alloweu when all atoms on one siue of the iotateu bonu aie active. Nultiple
ACTIvE lines can be piesent in the keyfile anu aie tieateu cumulatively. 0n each line the keywoiu
can be followeu by one oi moie atom numbeis oi atom ianges. The piesence of any ACTIvE keywoiu
oveiiiues any INACTIvE keywoius in the keyfile.

NPGYN a+*;Bb Sets the value of the " angle of a ciystal unit cell, &$!$, the angle between the b-axis
anu c-axis of a unit cell, oi, equivalently, the angle between the Y-axis anu Z-axis of a peiiouic box.
The uefault value in the absence of the ALPBA keywoiu is 9u uegiees.

N$-N$- a1 /34*X*+ M L +*;B)b This keywoiu pioviues the values foi a single angle-angle cioss
teim potential paiametei.

N$-N$-"&'O a$J$&cJ$PRb This keywoiu contiols use of the angle-angle cioss teim potential
eneigy. In the absence of a mouifying option, this keywoiu tuins on use of the potential. The N0NE
option tuins off use of this potential eneigy teim. The 0NLY option tuins off all potential eneigy
teims except foi this one.

34 "#$%&' ()*+,) -./0* 34
N$-N$-($#" a+*;Bb Sets the scale factoi neeueu to conveit the eneigy value computeu by the
angle-angle cioss teim potential into units of kcalmole. The coiiect value is foice fielu uepenuent
anu typically pioviueu in the heauei of the mastei foice fielu paiametei file. The uefault of (#18u)
2
= u.uuuSu46 is useu, if the ANuANu0NIT keywoiu is not given in the foice fielu paiametei file oi the
keyfile.

N$-P& aL /34*X*+) M W +*;B)b This keywoiu pioviues the values foi a single bonu angle benuing
paiametei. The integei mouifieis give the atom class numbeis foi the thiee kinus of atoms involveu
in the angle which is to be uefineu. The ieal numbei mouifieis give the foice constant value foi the
angle anu up to thiee iueal bonu angles in uegiees. In most cases only one iueal bonu angle is given,
anu that value is useu foi all occuiiences of the specifieu bonu angle. If all thiee iueal angles aie
given, the values apply when the cential atom of the angle is attacheu to u, 1 oi 2 auuitional hyuiogen
atoms, iespectively. This ``hyuiogen enviionment'' option is pioviueu to implement the
coiiesponuing featuie of Allingei's NN foice fielus. The uefault units foi the foice constant aie
kcalmoleiauian
2
, but this can be contiolleu via the ANuLE0NIT keywoiu.

N$-P&`?(V#? a+*;Bb Sets the value of the cubic teim in the Tayloi seiies expansion foim of the
bonu angle benuing potential eneigy. The ieal numbei mouifiei gives the value of the coefficient as a
multiple of the quauiatic coefficient. This teim multiplieu by the angle benuing eneigy unit
conveision factoi, the foice constant, anu the cube of the ueviation of the bonu angle fiom its iueal
value gives the cubic contiibution to the angle benuing eneigy. The uefault value in the absence of
the ANuLE-C0BIC keywoiu is zeio; &$!$, the cubic angle benuing teim is omitteu.

N$-P&`G&$"#? a+*;Bb Sets the value of the fifth powei teim in the Tayloi seiies expansion foim of
the bonu angle benuing potential eneigy. The ieal numbei mouifiei gives the value of the coefficient
as a multiple of the quauiatic coefficient. This teim multiplieu by the angle benuing eneigy unit
conveision factoi, the foice constant, anu the fifth powei of the ueviation of the bonu angle fiom its
iueal value gives the pentic contiibution to the angle benuing eneigy. The uefault value in the
absence of the ANuLE-PENTIC keywoiu is zeio; &$!$, the pentic angle benuing teim is omitteu.

N$-P&`K(N'"#? a+*;Bb Sets the value of the quaitic teim in the Tayloi seiies expansion foim of
the bonu angle benuing potential eneigy. The ieal numbei mouifiei gives the value of the coefficient
as a multiple of the quauiatic coefficient. This teim multiplieu by the angle benuing eneigy unit
conveision factoi, the foice constant, anu the foith powei of the ueviation of the bonu angle fiom its
iueal value gives the quaitic contiibution to the angle benuing eneigy. The uefault value in the
absence of the ANuLE-Q0ARTIC keywoiu is zeio; &$!$, the quaitic angle benuing teim is omitteu.

N$-P&`8&Q"#? a+*;Bb Sets the value of the sixth powei teim in the Tayloi seiies expansion foim of
the bonu angle benuing potential eneigy. The ieal numbei mouifiei gives the value of the coefficient
as a multiple of the quauiatic coefficient. This teim multiplieu by the angle benuing eneigy unit
conveision factoi, the foice constant, anu the sixth powei of the ueviation of the bonu angle fiom its
iueal value gives the sextic contiibution to the angle benuing eneigy. The uefault value in the absence
of the ANuLE-SEXTIC keywoiu is zeio; &$!$, the sextic angle benuing teim is omitteu.

N$-P&L aL /34*X*+) M W +*;B)b This keywoiu pioviues the values foi a single bonu angle benuing
paiametei specific to atoms in S-membeieu iings. The integei mouifieis give the atom class numbeis
foi the thiee kinus of atoms involveu in the angle which is to be uefineu. The ieal numbei mouifieis
give the foice constant value foi the angle anu up to thiee iueal bonu angles in uegiees. If all thiee
iueal angles aie given, the values apply when the cential atom of the angle is attacheu to u, 1 oi 2
auuitional hyuiogen atoms, iespectively. The uefault units foi the foice constant aie
kcalmoleiauian
2
, but this can be contiolleu via the ANuLE0NIT keywoiu. If any ANuLES keywoius
aie piesent, eithei in the mastei foice fielu paiametei file oi the keyfile, then TINKER iequiies that
35 "#$%&' ()*+,) -./0* 35
special ANuLES paiameteis be given foi all angles in S-membeieu iings. In the absence of any
ANuLES keywoius, stanuaiu ANuLE paiameteis will be useu foi bonus in S-membeieu iings.

N$-P&W aL /34*X*+) M W +*;B)b This keywoiu pioviues the values foi a single bonu angle benuing
paiametei specific to atoms in 4-membeieu iings. The integei mouifieis give the atom class numbeis
foi the thiee kinus of atoms involveu in the angle which is to be uefineu. The ieal numbei mouifieis
give the foice constant value foi the angle anu up to thiee iueal bonu angles in uegiees. If all thiee
iueal angles aie given, the values apply when the cential atom of the angle is attacheu to u, 1 oi 2
auuitional hyuiogen atoms, iespectively. The uefault units foi the foice constant aie
kcalmoleiauian
2
, but this can be contiolleu via the ANuLE0NIT keywoiu. If any ANuLE4 keywoius
aie piesent, eithei in the mastei foice fielu paiametei file oi the keyfile, then TINKER iequiies that
special ANuLE4 paiameteis be given foi all angles in 4-membeieu iings. In the absence of any
ANuLE4 keywoius, stanuaiu ANuLE paiameteis will be useu foi bonus in 4-membeieu iings.

N$-P&[ aL /34*X*+) M W +*;B)b This keywoiu pioviues the values foi a single bonu angle benuing
paiametei specific to atoms in S-membeieu iings. The integei mouifieis give the atom class numbeis
foi the thiee kinus of atoms involveu in the angle which is to be uefineu. The ieal numbei mouifieis
give the foice constant value foi the angle anu up to thiee iueal bonu angles in uegiees. If all thiee
iueal angles aie given, the values apply when the cential atom of the angle is attacheu to u, 1 oi 2
auuitional hyuiogen atoms, iespectively. The uefault units foi the foice constant aie
kcalmoleiauian
2
, but this can be contiolleu via the ANuLE0NIT keywoiu. If any ANuLES keywoius
aie piesent, eithei in the mastei foice fielu paiametei file oi the keyfile, then TINKER iequiies that
special ANuLES paiameteis be given foi all angles in S-membeieu iings. In the absence of any
ANuLES keywoius, stanuaiu ANuLE paiameteis will be useu foi bonus in S-membeieu iings.

N$-P&> aL /34*X*+) M L +*;B)b This keywoiu pioviues the values foi a single bonu angle benuing
paiametei foi a SBAPES-style Fouiiei potential function. The integei mouifieis give the atom class
numbeis foi the thiee kinus of atoms involveu in the angle which is to be uefineu. The ieal numbei
mouifieis give the foice constant value foi the angle, the angle shift in uegiees, anu the peiiouicity
value. Note that the foice constant shoulu be given as the ``haimonic'' value anu not the native
Fouiiei value. The uefault units foi the foice constant aie kcalmoleiauian
2
, but this can be
contiolleu via the ANuLE0NIT keywoiu.

N$-P&"&'O a$J$&cJ$PRb This keywoiu contiols use of the bonu angle benuing potential
eneigy teim. In the absence of a mouifying option, this keywoiu tuins on use of the potential. The
N0NE option tuins off use of this potential eneigy teim. The 0NLY option tuins off all potential
eneigy teims except foi this one.

N$-P&($#" a+*;Bb Sets the scale factoi neeueu to conveit the eneigy value computeu by the bonu
angle benuing potential into units of kcalmole. The coiiect value is foice fielu uepenuent anu
typically pioviueu in the heauei of the mastei foice fielu paiametei file. The uefault value of
(#18u)
2
= u.uuuSu46 is useu, if the ANuLE0NIT keywoiu is not given in the foice fielu paiametei
file oi the keyfile.

N$-ONQ a+*;Bb Set the maximum peimissible angle between the cuiient optimization seaich
uiiection anu the negative of the giauient uiiection. If this maximum angle value is exceeueu, the
optimization ioutine will note an eiioi conuition anu may iestait fiom the steepest uescent
uiiection. The uefault value in the absence of the ANuNAX keywoiu is usually 88 uegiees foi
conjugate giauient methous anu 18u uegiees (&$!$, uisableu) foi vaiiable metiic optimizations.

N$#8J`G'&88('& This keywoiu invokes use of full anisotiopic piessuie uuiing uynamics
simulations. When using this option, the thiee axis lengths anu axis angles vaiy sepaiately in
36 "#$%&' ()*+,) -./0* 36
iesponse to the piessuie tensoi. The uefault, in the absence of the keywoiu, is isotiopic piessuie
baseu on the aveiage of the uiagonal of the piessuie tensoi.

N'?Y#Z& This keywoiu causes TINKER moleculai uynamics-baseu piogiams to wiite tiajectoiies
uiiectly to a single plain-text aichive file with the .arc foimat. If an aichive file alieauy exists at the
stait of the calculation, then the newly geneiateu tiajectoiy is appenueu to the enu of the existing file.
The uefault in the absence of this keywoiu is to wiite the tiajectoiy snapshots to consecutively
numbeieu cycle files.

N"JO aD /34*X*+)U 3;C*U d.54*0 )4+/3XU /34*X*+U +*;B M /34*X*+b This keywoiu pioviues the
values neeueu to uefine a single foice fielu atom type.

V`NQ#8 a+*;Bb Sets the value of the b-axis length foi a ciystal unit cell, oi, equivalently, the Y-axis
length foi a peiiouic box. The length value in Angstioms is listeu aftei the keywoiu. If the keywoiu is
absent, the b-axis length is set equal to the a-axis length.

V`&QG"&'O a+*;Bb Sets the value of the ``B'' exponential factoi in the Buckingham van uei Waals
function, &$!$, the value of B in the foimula E
vuw
= ! { A exp|-B(R
o
R)j - C (R
o
R)
6
}.

VN'J8"N" aV&'&$I8&$b This keywoiu selects a baiostat algoiithm foi use uuiing moleculai
uynamics. At piesent only one mouifiei is available, a Beienusen bath coupling methou. The uefault
in the absence of the BAR0STAT keywoiu is to use the BERENBSEN algoiithm.

VN8#$ aD +*;B)b Piesence of this keywoiu tuins on a ``basin'' iestiaint potential function that
seives to uiive the system towaiu a compact stiuctuie. The actual function is a uaussian of the foim
E
basin
= $ A exp|-B R
2
j, summeu ovei all paiis of atoms wheie R is the uistance between atoms. The A
anu B values aie the uepth anu wiuth paiameteis given as mouifieis to the BASIN keywoiu. This
potential is cuiiently useu to contiol the uegiee of expansion uuiing potential eneigy smooth
pioceuuies thiough the use of shallow, bioau basins.

V&"N a+*;Bb Sets the value of the % angle of a ciystal unit cell, &$!$, the angle between the a-axis anu
c-axis of a unit cell, oi, equivalently, the angle between the X-axis anu Z-axis of a peiiouic box. The
uefault value in the absence of the BETA keywoiu is to set the % angle equal to the " angle as given by
the keywoiu ALPBA.

V#J"RG& a/34*X*+U 3;C*U d.54*0 )4+/3X M /34*X*+b This keywoiu pioviues the values to uefine
the coiiesponuence between a single biopolymei atom type anu its foice fielu atom type.

VJ$I aD /34*X*+) M D +*;B)b This keywoiu pioviues the values foi a single bonu stietching
paiametei. The integei mouifieis give the atom class numbeis foi the two kinus of atoms involveu in
the bonu which is to be uefineu. The ieal numbei mouifieis give the foice constant value foi the bonu
anu the iueal bonu length in -. The uefault units foi the foice constant aie kcalmole-
2
, but this can
be contiolleu via the B0NB0NIT keywoiu.

VJ$I`?(V#? a+*;Bb Sets the value of the cubic teim in the Tayloi seiies expansion foim of the
bonu stietching potential eneigy. The ieal numbei mouifiei gives the value of the coefficient as a
multiple of the quauiatic coefficient. This teim multiplieu by the bonu stietching eneigy unit
conveision factoi, the foice constant, anu the cube of the ueviation of the bonu length fiom its iueal
value gives the cubic contiibution to the bonu stietching eneigy. The uefault value in the absence of
the B0NB-C0BIC keywoiu is zeio; &$!$, the cubic bonu stietching teim is omitteu.
37 "#$%&' ()*+,) -./0* 37

VJ$I`K(N'"#? a+*;Bb Sets the value of the quaitic teim in the Tayloi seiies expansion foim of
the bonu stietching potential eneigy. The ieal numbei mouifiei gives the value of the coefficient as a
multiple of the quauiatic coefficient. This teim multiplieu by the bonu stietching eneigy unit
conveision factoi, the foice constant, anu the foith powei of the ueviation of the bonu length fiom its
iueal value gives the quaitic contiibution to the bonu stietching eneigy. The uefault value in the
absence of the B0NB-Q0ARTIC keywoiu is zeio; &$!$, the quaitic bonu stietching teim is omitteu.

VJ$IL aD /34*X*+) M D +*;B)b This keywoiu pioviues the values foi a single bonu stietching
paiametei specific to atoms in S-membeieu iings. The integei mouifieis give the atom class numbeis
foi the two kinus of atoms involveu in the bonu which is to be uefineu. The ieal numbei mouifieis
give the foice constant value foi the bonu anu the iueal bonu length in -. The uefault units foi the
foice constant aie kcalmole-
2
, but this can be contiolleu via the B0NB0NIT keywoiu. If any
B0NBS keywoius aie piesent, eithei in the mastei foice fielu paiametei file oi the keyfile, then
TINKER iequiies that special B0NBS paiameteis be given foi all bonus in S-membeieu iings. In the
absence of any B0NBS keywoius, stanuaiu B0NB paiameteis will be useu foi bonus in S-membeieu
iings.

VJ$IW aD /34*X*+) M D +*;B)b This keywoiu pioviues the values foi a single bonu stietching
paiametei specific to atoms in 4-membeieu iings. The integei mouifieis give the atom class numbeis
foi the two kinus of atoms involveu in the bonu which is to be uefineu. The ieal numbei mouifieis
give the foice constant value foi the bonu anu the iueal bonu length in -. The uefault units foi the
foice constant aie kcalmole-
2
, but this can be contiolleu via the B0NB0NIT keywoiu. If any
B0NB4 keywoius aie piesent, eithei in the mastei foice fielu paiametei file oi the keyfile, then
TINKER iequiies that special B0NB4 paiameteis be given foi all bonus in 4-membeieu iings. In the
absence of any B0NB4 keywoius, stanuaiu B0NB paiameteis will be useu foi bonus in 4-membeieu
iings

VJ$I[ aD /34*X*+) M D +*;B)b This keywoiu pioviues the values foi a single bonu stietching
paiametei specific to atoms in S-membeieu iings. The integei mouifieis give the atom class numbeis
foi the two kinus of atoms involveu in the bonu which is to be uefineu. The ieal numbei mouifieis
give the foice constant value foi the bonu anu the iueal bonu length in -. The uefault units foi the
foice constant aie kcalmole-
2
, but this can be contiolleu via the B0NB0NIT keywoiu. If any
B0NBS keywoius aie piesent, eithei in the mastei foice fielu paiametei file oi the keyfile, then
TINKER iequiies that special B0NBS paiameteis be given foi all bonus in S-membeieu iings. In the
absence of any B0NBS keywoius, stanuaiu B0NB paiameteis will be useu foi bonus in S-membeieu
iings

VJ$I"&'O a$J$&cJ$PRb This keywoiu contiols use of the bonu stietching potential eneigy
teim. In the absence of a mouifying option, this keywoiu tuins on use of the potential. The N0NE
option tuins off use of this potential eneigy teim. The 0NLY option tuins off all potential eneigy
teims except foi this one.

VJ$I"RG& a"NRPJ'cOJ'8&c-N(88#N$b Chooses the functional foim of the bonu stietching
potential. The TAYL0R option selects a Tayloi seiies expansion containing teims fiom haimonic
thiough quaitic. The N0RSE option selects a Noise potential fit to the iueal bonu length anu
stietching foice constant paiametei values. The uA0SSIAN option uses an inveiteu uaussian with
amplituue equal to the Noise bonu uissociation eneigy anu wiuth set to iepiouuce the vibiational
fiequency of a haimonic potential. The uefault is to use the TAYL0R potential.

VJ$I($#" a+*;Bb Sets the scale factoi neeueu to conveit the eneigy value computeu by the bonu
stietching potential into units of kcalmole. The coiiect value is foice fielu uepenuent anu typically
38 "#$%&' ()*+,) -./0* 38
pioviueu in the heauei of the mastei foice fielu paiametei file. The uefault value of 1.u is useu, if the
B0NB0NIT keywoiu is not given in the foice fielu paiametei file oi the keyfile.

?`NQ#8 a+*;Bb Sets the value of the C-axis length foi a ciystal unit cell, oi, equivalently, the Z-axis
length foi a peiiouic box. The length value in Angstioms is listeu aftei the keywoiu. If the keywoiu is
absent, the C-axis length is set equal to the A-axis length.

?`&QG"&'O a+*;Bb Sets the value of the ``C'' uispeision multipliei in the Buckingham van uei
Waals function, &$!$, the value of C in the foimula E
vuw
= ! { A exp|-B(R
o
R)j - C (R
o
R)
6
}.

?NGGN a+*;Bb This keywoiu is useu to set the noimal teimination ciiteiion foi the line seaich
phase of TINKER optimization ioutines. The line seaich exits successfully if the iatio of the cuiient
giauient piojection on the line to the piojection at the stait of the line seaich falls below the value of
CAPPA. A uefault value of u.1 is useu in the absence of the CAPPA keywoiu.

?YN'-& a1 /34*X*+ M 1 +*;Bb This keywoiu pioviues a value foi a single atomic paitial chaige
electiostatic paiametei. The integei mouifiei, if positive, gives the atom type numbei foi which the
chaige paiametei is to be uefineu. Note that chaige paiameteis aie given foi atom types, not atom
classes. If the integei mouifiei is negative, then the paiametei value to follow applies only to the
inuiviuual atom whose atom numbei is the negative of the mouifiei. The ieal numbei mouifiei gives
the values of the atomic paitial chaige in elections.

?YN'-&"&'O a$J$&cJ$PRb This keywoiu contiols use of the chaige-chaige potential eneigy
teim between paiis of atomic paitial chaiges. In the absence of a mouifying option, this keywoiu
tuins on use of the potential. The N0NE option tuins off use of this potential eneigy teim. The 0NLY
option tuins off all potential eneigy teims except foi this one.

?Y-`1D`8?NP& a+*;Bb This keywoiu pioviues a multiplicative scale factoi that is applieu to chaige-
chaige electiostatic inteiactions between 1-2 connecteu atoms, &$!$, atoms that aie uiiectly bonueu.
The uefault value of u.u is useu, if the CBu-12-SCALE keywoiu is not given in eithei the paiametei
file oi the keyfile.

?Y-`1L`8?NP& a+*;Bb This keywoiu pioviues a multiplicative scale factoi that is applieu to chaige-
chaige electiostatic inteiactions between 1-S connecteu atoms, &$!$, atoms sepaiateu by two covalent
bonus. The uefault value of u.u is useu, if the CBu-1S-SCALE keywoiu is not given in eithei the
paiametei file oi the keyfile.

?Y-`1W`8?NP& a+*;Bb This keywoiu pioviues a multiplicative scale factoi that is applieu to chaige-
chaige electiostatic inteiactions between 1-4 connecteu atoms, &$!$, atoms sepaiateu by thiee
covalent bonus. The uefault value of 1.u is useu, if the CBu-14-SCALE keywoiu is not given in eithei
the paiametei file oi the keyfile.

?Y-`1[`8?NP& a+*;Bb This keywoiu pioviues a multiplicative scale factoi that is applieu to chaige-
chaige electiostatic inteiactions between 1-S connecteu atoms, &$!$, atoms sepaiateu by foui covalent
bonus. The uefault value of 1.u is useu, if the CBu-1S-SCALE keywoiu is not given in eithei the
paiametei file oi the keyfile.

?Y-`?("J>> a+*;Bb Sets the cutoff uistance value in Angstioms foi chaige-chaige electiostatic
potential eneigy inteiactions. The eneigy foi any paii of sites beyonu the cutoff uistance will be set to
zeio. 0thei keywoius can be useu to select a smoothing scheme neai the cutoff uistance. The uefault
39 "#$%&' ()*+,) -./0* 39
cutoff uistance in the absence of the CBu-C0T0FF keywoiu is infinite foi nonpeiiouic systems anu
9.u foi peiiouic systems.

?Y-`"NG&' a+*;Bb This keywoiu allows mouification of the cutoff winuow foi chaige-chaige
electiostatic potential eneigy inteiactions. It is similai in foim anu action to the TAPER keywoiu,
except that its value applies only to the chaige-chaige potential. The uefault value in the absence of
the CBu-TAPER keywoiu is to begin the cutoff winuow at u.6S of the coiiesponuing cutoff uistance.

?Y-IGP"&'O a$J$&cJ$PRb This keywoiu contiols use of the chaige-uipole potential eneigy
teim between atomic paitial chaiges anu bonu uipoles. In the absence of a mouifying option, this
keywoiu tuins on use of the potential. The N0NE option tuins off use of this potential eneigy teim.
The 0NLY option tuins off all potential eneigy teims except foi this one.

?JPP#8#J$ a+*;Bb Sets the value of the ianuom collision fiequency useu in the Anueisen stochastic
collision uynamics theimostat. The supplieu value has units of fs
-1
atom
-1
anu is multiplieu inteinal
to TINKER by the time step in fs anu N
-2S
wheie N is the numbei of atoms. The uefault value useu in
the absence of the C0LLISI0N keywoiu is u.1 which is appiopiiate foi many systems but may neeu
aujustment to achieve auequate tempeiatuie contiol without peituibing the uynamics.

?JOG'&88 a+*;Bb Sets the value of the bulk solvent isotheimal compiessibility in Atm
-1
foi use
uuiing piessuie computation anu scaling in moleculai uynamics computations. The uefault value
useu in the absence of the C0NPRESS keywoiu is u.uuuu46, appiopiiate foi watei. This paiametei
seives as a scale factoi foi the uioningen-style piessuie bath coupling time, anu its exact value
shoulu not be of ciitical impoitance.

?("J>> a+*;Bb Sets the cutoff uistance value foi all nonbonueu potential eneigy inteiactions. The
eneigy foi any of the nonbonueu potentials of a paii of sites beyonu the cutoff uistance will be set to
zeio. 0thei keywoius can be useu to select a smoothing scheme neai the cutoff uistance, oi to apply
uiffeient cutoff uistances to vaiious nonbonueu eneigy teims.

I&V(- Tuins on piinting of uetaileu infoimation anu inteimeuiate values thioughout the piogiess
of a TINKER computation; not iecommenueu foi use with laige stiuctuies oi full potential eneigy
functions since a summaiy of eveiy inuiviuual inteiaction will usually be output.

I&>J'O a+*;Bb Sets the amount of uiffusion equation-style smoothing that will be applieu to the
potential eneigy suiface when using the SN00TB foice fielu. The ieal numbei option is equivalent to
the ``time'' value in the oiiginal Piela, !" ()$ foimalism; the laigei the value, the gieatei the smoothing.
The uefault value is zeio, meaning that no smoothing will be applieu.

I&-'&&8`>'&&IJO a/34*X*+b This keywoiu allows manual setting of the numbei of uegiees of
fieeuom uuiing a uynamics calculation. The integei mouifiei is useu by theimostating methous anu
in othei places as the numbei of uegiees of fieeuom, oveiiiuing the value ueteimineu by the TINKER
coue at uynamics staitup. In the absence of the keywoiu, the piogiams will automatically compute
the coiiect value baseu on the numbei of atoms active uuiing uynamics, bonu oi othei constiains,
anu use of peiiouic bounuaiy conuitions.

I&P"N`YNP-'&$ a+*;Bb Sets the value of the & paiametei in Balgien's buffeieu 14-7 vuw
potential eneigy functional foim. In the absence of the BELTA-BALuREN keywoiu, a uefault value of
u.u7 is useu.

40 "#$%&' ()*+,) -./0* 40
I#&P&?"'#? a+*;Bb Sets the value of the bulk uielectiic constant useu to uamp all electiostatic
inteiaction eneigies foi any of the TINKER electiostatic potential functions. The uefault value is foice
fielu uepenuent, but is usually equal to 1.u (foi Allingei's NN foice fielus the uefault is 1.S).

I#>>(8&`?YN'-& a+*;Bb This keywoiu is useu uuiing potential function smoothing pioceuuies to
specify the effective uiffusion coefficient to be applieu to the smootheu foim of the Coulomb's Law
chaige-chaige potential function. In the absence of the BIFF0SE-CBARuE keywoiu, a uefault value of
S.S is useu.

I#>>(8&`"J'8#J$ a+*;Bb This keywoiu is useu uuiing potential function smoothing pioceuuies
to specify the effective uiffusion coefficient to be applieu to the smootheu foim of the toision angle
potential function. In the absence of the BIFF0SE-T0RSI0N keywoiu, a uefault value of u.u22S is
useu.

I#>>(8&`ZI< a+*;Bb This keywoiu is useu uuiing potential function smoothing pioceuuies to
specify the effective uiffusion coefficient to be applieu to the smootheu uaussian appioximation to
the Lennaiu-}ones van uei Waals potential function. In the absence of the BIFF0SE-vBW keywoiu, a
uefault value of 1.u is useu.

I#-#"8 a/34*X*+b This keywoiu contiols the numbei of uigits of piecision output by TINKER in
iepoiting potential eneigies anu atomic cooiuinates. The alloweu values foi the integei mouifiei aie
4, 6 anu 8. Input values less than 4 will be set to 4, anu those gieatei than 8 will be set to 8. Final
eneigy values iepoiteu by most TINKER piogiams will contain the specifieu numbei of uigits to the
iight of the uecimal point. The numbei of uecimal places to be output foi atomic cooiuinates is
geneially two laigei than the value of BIuITS. In the absence of the BIuITS keywoiu a uefault value of
4 is useu, anu eneigies will be iepoiteu to 4 uecimal places with cooiuinates to 6 uecimal places.

I#GJP& aD /34*X*+) M D +*;B)b This keywoiu pioviues the values foi a single bonu uipole
electiostatic paiametei. The integei mouifieis give the atom type numbeis foi the two kinus of atoms
involveu in the bonu uipole which is to be uefineu. The ieal numbei mouifieis give the value of the
bonu uipole in Bebyes anu the position of the uipole site along the bonu. If the bonu uipole value is
positive, then the fiist of the two atom types is the positive enu of the uipole. Foi a negative bonu
uipole value, the fiist atom type listeu is negative. The position along the bonu is an optional mouifiei
that gives the postion of the uipole site as a fiaction between the fiist atom type (position=u) anu the
seconu atom type (position=1). The uefault foi the uipole position in the absence of a specifieu value
is u.S, placing the uipole at the miupoint of the bonu.

I#GJP&L aD /34*X*+) M D +*;B)b This keywoiu pioviues the values foi a single bonu uipole
electiostatic paiametei specific to atoms in S-membeieu iings. The integei mouifieis give the atom
type numbeis foi the two kinus of atoms involveu in the bonu uipole which is to be uefineu. The ieal
numbei mouifieis give the value of the bonu uipole in Bebyes anu the position of the uipole site along
the bonu. The uefault foi the uipole position in the absence of a specifieu value is u.S, placing the
uipole at the miupoint of the bonu. If any BIP0LES keywoius aie piesent, eithei in the mastei foice
fielu paiametei file oi the keyfile, then TINKER iequiies that special BIP0LES paiameteis be given
foi all bonu uipoles in S-membeieu iings. In the absence of any BIP0LES keywoius, stanuaiu BIP0LE
paiameteis will be useu foi bonus in S-membeieu iings.

I#GJP&W aD /34*X*+) M D +*;B)b This keywoiu pioviues the values foi a single bonu uipole
electiostatic paiametei specific to atoms in 4-membeieu iings. The integei mouifieis give the atom
type numbeis foi the two kinus of atoms involveu in the bonu uipole which is to be uefineu. The ieal
numbei mouifieis give the value of the bonu uipole in Bebyes anu the position of the uipole site along
the bonu. The uefault foi the uipole position in the absence of a specifieu value is u.S, placing the
41 "#$%&' ()*+,) -./0* 41
uipole at the miupoint of the bonu. If any BIP0LE4 keywoius aie piesent, eithei in the mastei foice
fielu paiametei file oi the keyfile, then TINKER iequiies that special BIP0LE4 paiameteis be given
foi all bonu uipoles in 4-membeieu iings. In the absence of any BIP0LE4 keywoius, stanuaiu BIP0LE
paiameteis will be useu foi bonus in 4-membeieu iings.

I#GJP&[ aD /34*X*+) M D +*;B)b This keywoiu pioviues the values foi a single bonu uipole
electiostatic paiametei specific to atoms in S-membeieu iings. The integei mouifieis give the atom
type numbeis foi the two kinus of atoms involveu in the bonu uipole which is to be uefineu. The ieal
numbei mouifieis give the value of the bonu uipole in Bebyes anu the position of the uipole site along
the bonu. The uefault foi the uipole position in the absence of a specifieu value is u.S, placing the
uipole at the miupoint of the bonu. If any BIP0LES keywoius aie piesent, eithei in the mastei foice
fielu paiametei file oi the keyfile, then TINKER iequiies that special BIP0LES paiameteis be given
foi all bonu uipoles in S-membeieu iings. In the absence of any BIP0LES keywoius, stanuaiu BIP0LE
paiameteis will be useu foi bonus in S-membeieu iings.

I#GJP&"&'O a$J$&cJ$PRb This keywoiu contiols use of the uipole-uipole potential eneigy
teim between paiis of bonu uipoles. In the absence of a mouifying option, this keywoiu tuins on use
of the potential. The N0NE option tuins off use of this potential eneigy teim. The 0NLY option tuins
off all potential eneigy teims except foi this one.

I#'&?"`11`8?NP& a+*;Bb This keywoiu pioviues a multiplicative scale factoi that is applieu to the
peimanent (uiiect) fielu uue to atoms within a polaiization gioup uuiing an inuuceu uipole
calculation, &$!$, atoms that aie in the same polaiization gioup as the atom being polaiizeu. The
uefault value of u.u is useu, if the BIRECT-11-SCALE keywoiu is not given in eithei the paiametei file
oi the keyfile.

I#'&?"`1D`8?NP& a+*;Bb This keywoiu pioviues a multiplicative scale factoi that is applieu to the
peimanent (uiiect) fielu uue to atoms in 1-2 polaiization gioups uuiing an inuuceu uipole
calculation, &$!$, atoms that aie in polaiization gioups uiiectly connecteu to the gioup containing the
atom being polaiizeu. The uefault value of u.u is useu, if the BIRECT-12-SCALE keywoiu is not given
in eithei the paiametei file oi the keyfile.

I#'&?"`1L`8?NP& a+*;Bb This keywoiu pioviues a multiplicative scale factoi that is applieu to the
peimanent (uiiect) fielu uue to atoms in 1-S polaiization gioups uuiing an inuuceu uipole
calculation, &$!$, atoms that aie in polaiization gioups sepaiateu by one gioup fiom the gioup
containing the atom being polaiizeu. The uefault value of u.u is useu, if the BIRECT-1S-SCALE
keywoiu is not given in eithei the paiametei file oi the keyfile.

I#'&?"`1W`8?NP& a+*;Bb This keywoiu pioviues a multiplicative scale factoi that is applieu to the
peimanent (uiiect) fielu uue to atoms in 1-4 polaiization gioups uuiing an inuuceu uipole
calculation, &$!$, atoms that aie in polaiization gioups sepaiateu by two gioups fiom the gioup
containing the atom being polaiizeu. The uefault value of 1.u is useu, if the BIRECT-14-SCALE
keywoiu is not given in eithei the paiametei file oi the keyfile.

I#Z&'-& a+*;Bb This keywoiu is useu by the SABBLE piogiam to set the maximum alloweu value
of the iatio of the giauient length along the path to the total giauient noim at the enu of a cycle of
minimization peipenuiculai to the path. If the value pioviueu by the BIvERuE keywoiu is exceeueu,
then anothei cycle of maximization along the path is iequiieu. A uefault value of u.uuS is useu in the
absence of the BIvERuE keywoiu.

IGP`?("J>> a+*;Bb Sets the cutoff uistance value in Angstioms foi bonu uipole-bonu uipole
electiostatic potential eneigy inteiactions. The eneigy foi any paii of bonu uipole sites beyonu the
42 "#$%&' ()*+,) -./0* 42
cutoff uistance will be set to zeio. 0thei keywoius can be useu to select a smoothing scheme neai the
cutoff uistance. The uefault cutoff uistance in the absence of the BPL-C0T0FF keywoiu is essentially
infinite foi nonpeiiouic systems anu 1u.u foi peiiouic systems.

IGP`"NG&' a+*;Bb This keywoiu allows mouification of the cutoff winuows foi bonu uipole-bonu
uipole electiostatic potential eneigy inteiactions. It is similai in foim anu action to the TAPER
keywoiu, except that its value applies only to the vuw potential. The uefault value in the absence of
the BPL-TAPER keywoiu is to begin the cutoff winuow at u.7S of the uipole cutoff uistance.

&?YJ a4*H4 )4+/3Xb The piesence of this keywoiu causes whatevei text follows it on the line to be
copieu uiiectly to the output file. This keywoiu is also active in paiametei files. It has no uefault
value; if no text follows the ECB0 keywoiu, a blank line is placeu in the output file.

&P&?"$&- aL /34*X*+) M 1 +*;Bb This keywoiu pioviues the values foi a single electionegativity
bonu length coiiection paiametei. The fiist two integei mouifieis give the atom class numbeis of the
atoms involveu in the bonu to be coiiecteu. The thiiu integei mouifiei is the atom class of an
electionegative atom. In the case of a piimaiy coiiection, an atom of this thiiu class must be uiiectly
bonueu to an atom of the seconu atom class. Foi a seconuaiy coiiection, the thiiu class is one atom
iemoveu fiom an atom of the seconu class. The ieal numbei mouifiei is the value in - by which the
oiiginal iueal bonu length is to be coiiecteu.

&$>J'?&`?Y#'NP#"R This keywoiu causes the chiiality founu at chiial tetiavalent centeis in the
input stiuctuie to be maintaineu uuiing TINKER calculations. The test foi chiiality is not exhaustive;
two iuentical monovalent atoms connecteu to a centei cause it to be maikeu as non-chiial, but laige
equivalent substituents aie not uetecteu. Tiivalent ``chiial'' centeis, foi example the alpha caibon in
uniteu-atom piotein stiuctuies, aie not enfoiceu as chiial.

&G8#PJ$'(P& a-&JO&"'#?cN'#"YO&"#?cYN'OJ$#?cYY-b This keywoiu selects the
combining iule useu to ueiive the ! value foi van uei Waals inteiactions. The uefault in the absence
of the EPSIL0NR0LE keywoiu is to use the uE0NETRIC mean of the inuiviuual ! values of the two
atoms involveu in the van uei Waals inteiaction.

&<NPI This keywoiu tuins on the use of Ewalu summation uuiing computation of electiostatic
inteiactions in peiiouic systems. In the cuiient veision of TINKER, iegulai Ewalu is useu foi
polaiizable atomic multipoles, anu smooth paiticle mesh Ewalu (PNE) is useu foi chaige-chaige
inteiactions. Ewalu summation is not available foi inteiactions involving bonu-centeieu uipoles. By
uefault, in the absence of the EWALB keywoiu, uistance-baseu cutoffs aie useu foi electiostatic
inteiactions.

&<NPI`NPGYN a+*;Bb Sets the value of the Ewalu coefficient which contiols the wiuth of the
uaussian scieening chaiges uuiing paiticle mesh Ewalu summation. In the absence of the EWALB-
ALPBA keywoiu, a value is chosen which causes inteiactions outsiue the ieal-space cutoff to be
below a fixeu toleiance. Foi most stanuaiu applications of Ewalu summation, the piogiam uefault
shoulu be useu.

&<NPI`VJ($IN'R This keywoiu invokes the use of insulating (&!; vacuum) bounuaiy conuitions
uuiing Ewalu summation, coiiesponuing to the meuia suiiounuing the system having a uielectiic
value of 1. The uefault in the absence of the EWALB-B00NBARY keywoiu is to use conuucting (&!;
tinfoil) bounuaiy conuitions wheie the suiiounuing meuia is assumeu to have an infinite uielectiic
value.

43 "#$%&' ()*+,) -./0* 43
&<NPI`?("J>> a+*;Bb Sets the value in Angstioms of the ieal-space uistance cutoff foi use uuiing
Ewalu summation. By uefault, in the absence of the EWALB-C0T0FF keywoiu, a value of 9.u is useu.

&Q#"`GN(8& This keywoiu causes TINKER piogiams to pause anu wait foi a caiiiage ietuin at the
enu of executation piioi to ietuining contiol to the opeiating system. This is useful to keep the
execution winuow open following teimination on machines iunning Niciosoft Winuows oi Apple
Nac0S. The uefault in the absence of the EXIT-PA0SE keywoiu, is to ietuin contiol to the opeiating
system immeuiately at piogiam teimination.

&Q"'N"&'O a$J$&cJ$PRb This keywoiu contiols use of the usei uefineu extia potential eneigy
teim. In the absence of a mouifying option, this keywoiu tuins on use of the potential. The N0NE
option tuins off use of this potential eneigy teim. The 0NLY option tuins off all potential eneigy
teims except foi this one.

>?"O#$ a+*;Bb This keywoiu sets a conveigence ciiteiion foi successful completion of a TINKER
optimization. If the value of the optimization objective function, typically the potential eneigy, falls
below the value set by FCTNIN, then the optimization is ueemeu to have conveigeu. The uefault
value in the absence of the FCTNIN keywoiu is -1uuuuuu, effectively iemoving this ciiteiion as a
possible agent foi teimination.

>J'?&>#&PI a3;C*b This keywoiu pioviues a name foi the foice fielu to be useu in the cuiient
calculation. Its value is usually set in the mastei foice fielu paiametei file foi the calculation (see the
PARANETERS keywoiu) insteau of in the keyfile.

>'#?"#J$ a+*;Bb Sets the value of the fiictional coefficient in ps
-1
foi use with stochastic uynamics.
The uefault value useu in the absence of the FRICTI0N keywoiu is 91.u, which is geneially
appiopiiate foi watei.

>'#?"#J$`8?NP#$- This keywoiu tuins on the use of atomic suiface aiea-baseu scaling of the
fiictional coefficient uuiing stochastic uynamics. When in use, the coefficient foi each atom is
multiplieu by that atom's fiaction of exposeu suiface aiea. The uefault in the absence of the keywoiu
is to omit the scaling anu use the full coefficient value foi each atom.

-NOON a+*;Bb Sets the value of the ' angle of a ciystal unit cell, &$!$, the angle between the a-axis
anu b-axis of a unit cell, oi, equivalently, the angle between the X-axis anu Y-axis of a peiiouic box.
The uefault value in the absence of the uANNA keywoiu is to set the ' angle equal to the " angle as
given by the keywoiu ALPBA.

-NOON`YNP-'&$ a+*;Bb Sets the value of the ' paiametei in Balgien's buffeieu 14-7 vuw
potential eneigy functional foim. In the absence of the BELTA-BALuREN keywoiu, a uefault value of
u.12 is useu.

-NOONO#$ a+*;Bb Sets the conveigence taiget value foi ' uuiing seaiches foi maxima along the
quauiatic synchionous tiansit useu by the SABBLE piogiam. The value of ' is the squaie of the iatio
of the giauient piojection along the path to the total giauient. A uefault value of u.uuuu1 is useu in
the absence of the uANNANIN keywoiu.

-N(88"RG& aPe`DcPe`WcOOD`DcOOL`Dc#$`GPN?&b This keywoiu specifies the unueilying vuw
foim that a uaussian vuw appioximation will attempt to fit.numbei of teims to be useu in a uaussian
appioximation of the Lennaiu-}ones van uei Waals potential. The text mouifiei gives the name of the
functional foim to be useu. Thus L}-2 as a mouifiei will iesult in a 2-uaussian fit to a Lennaiu-}ones
44 "#$%&' ()*+,) -./0* 44
vuw potential. The uA0SSTYPE keywoiu only takes effect when vBWTYPE is set to uA0SSIAN. This
keywoiu has no uefault value.

-'J(G a/34*X*+U /34*X*+ B/)4b This keywoiu uefines an atom gioup as a substiuctuie within the
full input moleculai stiuctuie. The value of the fiist integei is the gioup numbei which must be in the
iange fiom 1 to the maximum numbei of alloweu gioups. The iemaining inteigeis give the atom oi
atoms containeu in this gioup as one oi moie atom numbeis oi ianges. Nultiple keywoiu lines can
be useu to specify auuitional atoms in the same gioup. Note that an atom can only be in one gioup,
the last gioup to which it is assigneu is the one useu.

-'J(G`#$"&' This keywoiu assigns a value of 1.u to all intei-gioup inteiactions anu a value of u.u
to all intia-gioup inteiactions. Foi example, combination with the uR00P-N0LEC0LE keywoiu
pioviues foi iigiu-bouy calculations.

-'J(G`#$"'N This keywoiu assigns a value of 1.u to all intia-gioup inteiactions anu a value of
u.u to all intei-gioup inteiactions.

-'J(G`OJP&?(P& This keywoiu sets each inuiviuual molecule in the system to be a sepaiate
atom gioup, but uoes not assign weights to gioup-gioup inteiactions.

-'J(G`8&P&?" aD /34*X*+)U +*;Bb This keywoiu gives the weight in the final potential eneigy of a
specifieu set of intia- oi inteigioup inteiactions. The integei mouifieis give the gioup numbeis of the
gioups involveu. If the two numbeis aie the same, then an intiagioup set of inteiactions is specifieu.
The ieal mouifiei gives the weight by which all eneigetic inteiactions in this set will be multiplieu
befoie incoipoiation into the final potential eneigy. If omitteu as a keywoiu mouifiei, the weight will
be set to 1.u by uefault. If any SELECT-uR00P keywoius aie piesent, then any set of inteiactions not
specifieu in a SELECT-uR00P keywoiu is given a zeio weight. The uefault when no SELECT-uR00P
keywoius aie specifieu is to use all inteigioup inteiactions with a weight of 1.u anu to set all
intiagioup inteiactions to zeio.

YVJ$I aD /34*X*+) M D +*;B)b This keywoiu pioviues the values foi the NNS-style uiiectional
hyuiogen bonuing paiameteis foi a single paii of atoms. The integei mouifieis give the paii of atom
class numbeis foi which hyuiogen bonuing paiameteis aie to be uefineu. The two ieal numbei
mouifieis give the values of the minimum eneigy contact uistance in - anu the well uepth at the
minimum uistance in kcalmole.

Y&88`?("J>> a+*;Bb This keywoiu uefines a lowei limit foi significant Bessian matiix elements.
Buiing computation of the Bessian matiix of paitial seconu ueiivatives, any matiix elements with
absolute value below BESS-C0T0FF will be set to zeio anu omitteu fiom the spaise matiix Bessian
stoiage scheme useu by TINKER. Foi most calculations, the uefault in the absence of this keywoiu is
zeio, i.e., all elements will be stoieu. Foi most Tiuncateu Newton optimizations the Bessian cutoff
will be chosen uynamically by the optimizei.

Y-(&88 a+*;Bb Sets an initial guess foi the aveiage value of the uiagonal elements of the scaleu
inveise Bessian matiix useu by the optimally conuitioneu vaiiable metiic optimization ioutine. A
uefault value of u.4 is useu in the absence of the Bu0ESS keywoiu.

#OG'JG&' aW /34*X*+) M D +*;B)b This keywoiu pioviues the values foi a single CBARNN-style
impiopei uiheuial angle paiametei.

45 "#$%&' ()*+,) -./0* 45
#OG'JG"&'O a$J$&cJ$PRb This keywoiu contiols use of the CBARNN-style impiopei uiheuial
angle potential eneigy teim. In the absence of a mouifying option, this keywoiu tuins on use of the
potential. The N0NE option tuins off use of this potential eneigy teim. The 0NLY option tuins off all
potential eneigy teims except foi this one.

#OG'JG($#" a+*;Bb Sets the scale factoi neeueu to conveit the eneigy value computeu by the
CBARNN-style impiopei uiheuial angle potential into units of kcalmole. The coiiect value is foice
fielu uepenuent anu typically pioviueu in the heauei of the mastei foice fielu paiametei file. The
uefault value of 1.u is useu, if the INPR0P0NIT keywoiu is not given in the foice fielu paiametei file
oi the keyfile.

#OG"J'8 aW /34*X*+) M .@ 45 L +*;Bc+*;Bc/34*X*+ 4+/@B*)b This keywoiu pioviues the values foi
a single ANBER-style impiopei toisional angle paiametei. The fiist foui integei mouifieis give the
atom class numbeis foi the atoms involveu in the impiopei toisional angle to be uefineu. By
convention, the thiiu atom class of the foui is the tiigonal atom on which the impiopei toision is
centeieu. The toisional angle computeu is liteially that uefineu by the foui atom classes in the oiuei
specifieu by the keywoiu. Each of the iemaining tiiples of iealiealintegei mouifieis give the half-
amplituue, phase offset in uegiees anu peiiouicity of a paiticulai impiopei toisional teim,
iespectively. Peiiouicities thiough S-folu aie alloweu foi impiopei toisional paiameteis.

#OG"J'8"&'O a$J$&cJ$PRb This keywoiu contiols use of the ANBER-style impiopei toisional
angle potential eneigy teim. In the absence of a mouifying option, this keywoiu tuins on use of the
potential. The N0NE option tuins off use of this potential eneigy teim. The 0NLY option tuins off all
potential eneigy teims except foi this one.

#OG"J'8($#" a+*;Bb Sets the scale factoi neeueu to conveit the eneigy value computeu by the
ANBER-style impiopei toisional angle potential into units of kcalmole. The coiiect value is foice
fielu uepenuent anu typically pioviueu in the heauei of the mastei foice fielu paiametei file. The
uefault value of 1.u is useu, if the INPT0RS0NIT keywoiu is not given in the foice fielu paiametei file
oi the keyfile.

#$N?"#Z& a/34*X*+ B/)4b Sets the list of inactive atoms uuiing a TINKER computation. Inuiviuual
potential eneigy teims aie not computeu when all atoms involveu in the teim aie inactive. Foi
Caitesian space calculations, inactive atoms aie not alloweu to move. Foi toisional space
calculations, iotations aie not alloweu when theie aie inactive atoms on both siues of the iotateu
bonu. Nultiple INACTIvE lines can be piesent in the keyfile, anu on each line the keywoiu can be
followeu by one oi moie atom numbeis oi ianges. If any INACTIvE keys aie founu, all atoms aie set
to active except those listeu on the INACTIvE lines. The ACTIvE keywoiu oveiiiues all INACTIvE
keywoius founu in the keyfile.

#$"&-'N"& aZ&'P&"cV&&ON$c8"J?YN8"#?c'#-#IVJIRb Chooses the integiation methou foi
piopagation of uynamics tiajectoiies. The keywoiu is followeu on the same line by the name of the
option. Stanuaiu Newtonian NB can be iun using eithei vERLET foi the velocity veilet methou, oi
BEENAN foi the velocity foim of Beinie Biook's ``Bettei Beeman'' methou. A velocity veilet-baseu
stochastic uynamics tiajectoiy is selecteu by the ST0CBASTIC mouifiei. A iigiu-bouy uynamics
methou is selecteu by the RIuIBB0BY mouifiei. The uefault integiation scheme is NB using the
BEENAN methou.

#$"ONQ a/34*X*+b Sets the maximum numbei of inteipolation cycles that will be alloweu uuiing
the line seaich phase of an optimization. All giauient-baseu TINKER optimization ioutines use a
common line seaich ioutine involving quauiatic extiapolation anu cubic inteipolation. If the value of
INTNAX is ieacheu, an eiioi status is set foi the line seaich anu the seaich is iepeateu with a much
46 "#$%&' ()*+,) -./0* 46
smallei initial step size. The uefault value in the absence of this keywoiu is optimization ioutine
uepenuent, but is usually in the iange S to 1u.

PNOVIN a+*;Bb This keywoiu sets the value of the ( path paiametei foi fiee eneigy peituibation
calculations. The ieal numbei mouifiei specifies the position along the mutation path anu must be a
numbei in the iange fiom u (initial state) to 1 (final state). The actual atoms involveu in the mutation
aie given sepaiately in inuiviuual N0TATE keywoiu lines.

PV>-8`Z&?"J'8 a/34*X*+b Sets the numbei of coiiection vectois useu by the limiteu-memoiy L-
BFuS optimization ioutine. The cuiient maximum allowable value, anu the uefault in the absence of
the LBFuS-vECT0RS keywoiu is 1S.

P#-Y"8 This keywoiu tuins on Nethou of Lights neighboi geneiation foi the paitial chaige
electiostatics anu any of the van uei Waals potentials. This methou will yielu iuentical eneigetic
iesults to the stanuaiu uouble loop methou. Nethou of Lights will be fastei when the volume of a
spheie with iauius equal to the nonbonu cutoff uistance is significantly less than half the volume of
the total system (&$!$, the full moleculai system, the ciystal unit cell oi the peiiouic box). It iequiies
less stoiage than paiiwise neighboi lists.

P#8"`V(>>&' a+*;Bb Sets the size of the neighboi list buffei in Angstioms. This value is auueu to
the actual cutoff uistance to ueteimine which paiis will be kept on the neighboi list. The same buffei
value is useu foi all neighboi lists. The uefault value in the absence of 2.u is useu in the absence of the
LIST-B0FFER keywoiu.

ONQ#"&' a/34*X*+b Sets the maximum numbei of minimization iteiations that will be alloweu foi
any TINKER piogiam that uses any of the nonlineai optimization ioutines. The uefault value in the
absence of this keywoiu is piogiam uepenuent, but is always set to a veiy laige numbei.

O&"NP This keywoiu pioviues the values foi a single tiansition metal liganu fielu paiametei. ()*+
*-." /+01)23 ." 42+"+5* .5 *-+ 6)3+7 89* 5)* :6*.!+ .5 *-+ 6922+5* !+2".)5 ); <=(>?@A

O&"NP"&'O a$J$&cJ$PRb This keywoiu contiols use of the tiansition metal liganu fielu
potential eneigy teim. In the absence of a mouifying option, this keywoiu tuins on use of the
potential. The N0NE option tuins off use of this potential eneigy teim. The 0NLY option tuins off all
potential eneigy teims except foi this one.

OOD`8"'V$I This keywoiu switches the behavioi of the stietch-benu potential function to match
the foimulation useu by the NN2 foice fielu. In NN2, stietching of bonus to attacheu hyuiogen
atoms is not incluuing in computing the stietch-benu cioss teim eneigy. The uefault behavioi in the
absence of this keywoiu is to incluue stietching of attacheu hyuiogen atoms as in the NNS foice
fielu.

OGJP&`1D`8?NP& a+*;Bb This keywoiu pioviues a multiplicative scale factoi that is applieu to
peimanent atomic multipole electiostatic inteiactions between 1-2 connecteu atoms, &$!$, atoms that
aie uiiectly bonueu. The uefault value of u.u is useu, if the NP0LE-12-SCALE keywoiu is not given in
eithei the paiametei file oi the keyfile.

OGJP&`1L`8?NP& a+*;Bb This keywoiu pioviues a multiplicative scale factoi that is applieu to
peimanent atomic multipole electiostatic inteiactions between 1-S connecteu atoms, &$!$, atoms
sepaiateu by two covalent bonus. The uefault value of u.u is useu, if the NP0LE-1S-SCALE keywoiu is
not given in eithei the paiametei file oi the keyfile.
47 "#$%&' ()*+,) -./0* 47

OGJP&`1W`8?NP& a+*;Bb This keywoiu pioviues a multiplicative scale factoi that is applieu to
peimanent atomic multipole electiostatic inteiactions between 1-4 connecteu atoms, &$!$, atoms
sepaiateu by thiee covalent bonus. The uefault value of 1.u is useu, if the NP0LE-14-SCALE keywoiu
is not given in eithei the paiametei file oi the keyfile.

OGJP&`1[`8?NP& a+*;Bb This keywoiu pioviues a multiplicative scale factoi that is applieu to
peimanent atomic multipole electiostatic inteiactions between 1-S connecteu atoms, &$!$, atoms
sepaiateu by foui covalent bonus. The uefault value of 1.u is useu, if the NP0LE-1S-SCALE keywoiu
is not given in eithei the paiametei file oi the keyfile.

OGJP&`?("J>> a+*;Bb Sets the cutoff uistance value in Angstioms foi atomic multipole potential
eneigy inteiactions. The eneigy foi any paii of sites beyonu the cutoff uistance will be set to zeio.
0thei keywoius can be useu to select a smoothing scheme neai the cutoff uistance. The uefault cutoff
uistance in the absence of the NP0LE-C0T0FF keywoiu is infinite foi nonpeiiouic systems anu 9.u
foi peiiouic systems.

OGJP&`"NG&' a+*;Bb This keywoiu allows mouification of the cutoff winuow foi atomic multipole
potential eneigy inteiactions. It is similai in foim anu action to the TAPER keywoiu, except that its
value applies only to the atomic multipole potential. The uefault value in the absence of the NP0LE-
TAPER keywoiu is to begin the cutoff winuow at u.6S of the coiiesponuing cutoff uistance.

OGJP&"&'O a$J$&cJ$PRb This keywoiu contiols use of the atomic multipole electiostatics
potential eneigy teim. In the absence of a mouifying option, this keywoiu tuins on use of the
potential. The N0NE option tuins off use of this potential eneigy teim. The 0NLY option tuins off all
potential eneigy teims except foi this one.

O(P"#GJP& a[ B/3*) :/47f L 5+ W /34*X*+) M 1 +*;Bg L +*;B)g 1 +*;Bg D +*;B)g L +*;B)b This
keywoiu pioviues the values foi a set of atomic multipole paiameteis at a single site. A complete
keywoiu entiy consists of thiee consequtive lines, the fiist line containing the N0LTIP0LE keywoiu
anu the two following lines. The fiist line contains thiee integeis which uefine the atom type on
which the multipoles aie centeieu, anu the Z-axis anu X-axis uefining atom types foi this centei. The
optional fouith integei contains the Y-axis uefining atom type, anu is only iequiieu foi locally chiial
multipole sites. The ieal numbei on the fiist line gives the monopole (atomic chaige) in elections.
The seconu line contains thiee ieal numbeis which give the X-, Y- anu Z-components of the atomic
uipole in election--. The final thiee lines, consisting of one, two anu thiee ieal numbeis give the
uppei tiiangle of the tiaceless atomic quauiupole tensoi in election--
2
.

O("N"& aL /34*X*+)b This keywoiu is useu to specify atoms to be mutateu uuiing fiee eneigy
peituibation calculations. The fiist integei mouifiei gives the atom numbei of an atom in the cuiient
system. The final two mouifiei values give the atom types coiiesponuing the the (=u anu (=1 states
of the specifieu atom.

O("(NP`11`8?NP& a+*;Bb This keywoiu pioviues a multiplicative scale factoi that is applieu to
the inuuceu (mutual) fielu uue to atoms within a polaiization gioup uuiing an inuuceu uipole
calculation, &$!$, atoms that aie in the same polaiization gioup as the atom being polaiizeu. The
uefault value of 1.u is useu, if the N0T0AL-11-SCALE keywoiu is not given in eithei the paiametei
file oi the keyfile.

O("(NP`1D`8?NP& a+*;Bb This keywoiu pioviues a multiplicative scale factoi that is applieu to
the inuuceu (mutual) fielu uue to atoms in 1-2 polaiization gioups uuiing an inuuceu uipole
48 "#$%&' ()*+,) -./0* 48
calculation, &$!$, atoms that aie in polaiization gioups uiiectly connecteu to the gioup containing the
atom being polaiizeu. The uefault value of 1.u is useu, if the N0T0AL-12-SCALE keywoiu is not given
in eithei the paiametei file oi the keyfile.

O("(NP`1L`8?NP& a+*;Bb This keywoiu pioviues a multiplicative scale factoi that is applieu to
the inuuceu (mutual) fielu uue to atoms in 1-S polaiization gioups uuiing an inuuceu uipole
calculation, &$!$, atoms that aie in polaiization gioups sepaiateu by one gioup fiom the gioup
containing the atom being polaiizeu. The uefault value of 1.u is useu, if the N0T0AL-1S-SCALE
keywoiu is not given in eithei the paiametei file oi the keyfile.

O("(NP`1W`8?NP& a+*;Bb This keywoiu pioviues a multiplicative scale factoi that is applieu to
the inuuceu (mutual) fielu uue to atoms in 1-4 polaiization gioups uuiing an inuuceu uipole
calculation, &$!$, atoms that aie in polaiization gioups sepaiateu by two gioups fiom the gioup
containing the atom being polaiizeu. The uefault value of 1.u is useu, if the N0T0AL-14-SCALE
keywoiu is not given in eithei the paiametei file oi the keyfile.

$&#-YVJ'`-'J(G8 This keywoiu causes the attacheu atom to be useu in ueteimining the
chaige-chaige neighboi uistance foi all monovalent atoms in the moleculai system. Its use causes all
monovalent atoms to be tieateu the same as theii attacheu atoms foi puiposes of incluuing oi scaling
1-2, 1-S anu 1-4 inteiactions. This option woiks only foi the simple chaige-chaige electiostatic
potential; it uoes not affect bonu uipole oi atomic multipole potentials. The NEIuBB0R-uR00PS
scheme is similai to that useu by some common foice fielus such as ENCAB.

$&#-YVJ'`P#8" This keywoiu tuins on paiiwise neighboi lists foi paitial chaige electiostatics,
polaiize multipole electiostatics anu any of the van uei Waals potentials. This methou will yielu
iuentical eneigetic iesults to the stanuaiu uouble loop methou.

$&("'NP`-'J(G8 This keywoiu causes the attacheu atom to be useu in ueteimining the chaige-
chaige inteiaction cutoff uistance foi all monovalent atoms in the moleculai system. Its use ieuuces
cutoff uiscontinuities by avoiuing splitting many of the laigest chaige sepaiations founu in typical
molecules. Note that this keywoiu uoes not iigoiously implement the usual concept of a ``neutial
gioup'' as useu in the liteiatuie with ANBER0PLS anu othei foice fielus. This option woiks only foi
the simple chaige-chaige electiostatic potential; it uoes not affect bonu uipole oi atomic multipole
potentials.

$&<Y&88 a/34*X*+b Sets the numbei of algoiithmic iteiations between iecomputation of the
Bessian matiix. At piesent this keywoiu applies exclusively to optimizations using the Tiuncateu
Newton methou. The uefault value in the absence of this keywoiu is 1, &$!$; the Bessian is computeu
on eveiy iteiation.

$&Q"#"&' a/34*X*+b Sets the iteiation numbei to be useu foi the fiist iteiation of the cuiient
computation. At piesent this keywoiu applies to optimization pioceuuies wheie its use can effect
conveigence ciiteiia, timing of iestaits, anu so foith. The uefault in the absence of this keywoiu is to
take the initial iteiation as iteiation 1.

$J8&`ON88 a+*;Bb This keywoiu sets the mass of paiticles making up the Nose-Boovei chain in
that theimostating methou. The uefault in the absence of the N0SE-NASS keywoiu is to use a mass of
u.1.

$JZ&'8#J$ Tuins off the use of veision numbeis appenueu to the enu of filenames as the methou
foi geneiating filenames foi upuateu copies of an existing file. The piesence of this keywoiu iesults
in uiiect use of input file names without a seaich foi the highest available veision, anu iequiies the
49 "#$%&' ()*+,) -./0* 49
entiy of specific output file names in many auuitional cases. By uefault, in the absence of this
keywoiu, TINKER geneiates anu attaches veision numbeis in a mannei similai to the Bigital
0penvNS opeiating system. Foi example, subsequent new veisions of the file molecule.xyz
woulu be wiitten fiist to the file molecule.xyz_2, then to molecule.xyz_3, !"#.

J?"NY&I'J$ Specifies that the peiiouic ``box'' is a tiuncateu octaheuion with maximal uistance
acioss the tiuncateu octaheuion as given by the A-AXIS keywoiu. All othei unit cell anu peiiouic box
size-uefining keywoius aie ignoieu if the 0CTABEBR0N keywoiu is piesent.

JGV&$I aD /34*X*+) M 1 +*;Bb This keywoiu pioviues the values foi a single Allingei NN-style
out-of-plane angle benuing potential paiametei. The fiist integei mouifiei is the atom class of the
cential tiigonal atom anu the seconu integei is the atom class of the out-of-plane atom. The ieal
numbei mouifiei gives the foice constant value foi the out-of-plane angle. The uefault units foi the
foice constant aie kcalmoleiauian
2
, but this can be contiolleu via the 0PBENB0NIT keywoiu.

JGV&$I"&'O a$J$&cJ$PRb This keywoiu contiols use of the Allingei NN-style out-of-plane
benuing potential eneigy teim. In the absence of a mouifying option, this keywoiu tuins on use of the
potential. The N0NE option tuins off use of this potential eneigy teim. The 0NLY option tuins off all
potential eneigy teims except foi this one.

JGV&$I($#" a+*;Bb Sets the scale factoi neeueu to conveit the eneigy value computeu by the
Allingei NN-style out-of-plane benuing potential into units of kcalmole. The coiiect value is foice
fielu uepenuent anu typically pioviueu in the heauei of the mastei foice fielu paiametei file. The
uefault of (#18u)
2
= u.uuuSu46 is useu, if the 0PBENB0NIT keywoiu is not given in the foice fielu
paiametei file oi the keyfile.

JGI#8" aW /34*X*+) M 1 +*;Bb This keywoiu pioviues the values foi a single out-of-plane uistance
potential paiametei. The fiist integei mouifiei is the atom class of the cential tiigonal atom anu the
thiee following integei mouifieis aie the atom classes of the thiee attacheu atoms. The ieal numbei
mouifiei is the foice constant foi the haimonic function of the out-of-plane uistance of the cential
atom. The uefault units foi the foice constant aie kcalmole-
2
, but this can be contiolleu via the
0PBIST0NIT keywoiu.

JGI#8""&'O a$J$&cJ$PRb This keywoiu contiols use of the out-of-plane uistance potential
eneigy teim. In the absence of a mouifying option, this keywoiu tuins on use of the potential. The
N0NE option tuins off use of this potential eneigy teim. The 0NLY option tuins off all potential
eneigy teims except foi this one.

JGI#8"($#" a+*;Bb Sets the scale factoi neeueu to conveit the eneigy value computeu by the out-
of-plane uistance potential into units of kcalmole. The coiiect value is foice fielu uepenuent anu
typically pioviueu in the heauei of the mastei foice fielu paiametei file. The uefault value of 1.u is
useu, if the 0PBIST0NIT keywoiu is not given in the foice fielu paiametei file oi the keyfile.

JZ&'<'#"& Causes TINKER piogiams, such as minimizations, that output inteimeuiate
cooiuinate sets to cieate a single uisk file foi the inteimeuiate iesults which is successively
oveiwiitten with the new inteimeuiate cooiuinates as they become available. This keywoiu is
essentially the opposite of the SAvECYCLE keywoiu.

GN'NO&"&'8 a9/B* 3;C*b Pioviues the name of the foice fielu paiametei file to be useu foi the
cuiient TINKER calculation. The stanuaiu file name extension foi paiametei files, .prm, is an
optional pait of the file name mouifiei. The uefault in the absence of the PARANETERS keywoiu is to
50 "#$%&' ()*+,) -./0* 50
look foi a paiametei file with the same base name as the moleculai system anu enuing in the .prm
extension. If a valiu paiametei file is not founu, the usei will askeu to pioviue a file name
inteiactively.

G#N"JO a1 /34*X*+ M L +*;B)b This keywoiu pioviues the values foi the pisystem N0 potential
paiameteis foi a single atom class belonging to a pisystem.

G#VJ$I aD /34*X*+) M D +*;B)b This keywoiu pioviues the values foi the pisystem N0 potential
paiameteis foi a single type of pisystem bonu.

G#VJ$IW aD /34*X*+) M D +*;B)b This keywoiu pioviues the values foi the pisystem N0 potential
paiameteis foi a single type of pisystem bonu containeu in a 4-membeieu iing.

G#VJ$I[ aD /34*X*+) M D +*;B)b This keywoiu pioviues the values foi the pisystem N0 potential
paiameteis foi a single type of pisystem bonu containeu in a S-membeieu iing.

G#8R8"&O a/34*X*+ B/)4b This keywoiu sets the atoms within a molecule that aie pait of a
conjugateu #-system. The keywoiu is followeu on the same line by a list of atom numbeis anuoi
atom ianges that constitute the #-system. The Allingei NN foice fielus use this infoimation to set up
an N0 calculation useu to scale bonu anu toision paiameteis involving #-system atoms.

G#"J'8 aD /34*X*+) M 1 +*;Bb This keywoiu pioviues the values foi a single pi-oibital toisional
angle potential paiametei. The two integei mouifieis give the atom class numbeis foi the atoms
involveu in the cential bonu of the toisional angle to be paiameteiizeu. The ieal mouifiei gives the
value of the 2-folu Fouiiei amplituue foi the toisional angle between p-oibitals centeieu on the
uefineu bonu atom classes. The uefault units foi the stietch-toision foice constant can be contiolleu
via the PIT0RS0NIT keywoiu.

G#"J'8"&'O a$J$&cJ$PRb This keywoiu contiols use of the pi-oibital toisional angle potential
eneigy teim. In the absence of a mouifying option, this keywoiu tuins on use of the potential. The
N0NE option tuins off use of this potential eneigy teim. The 0NLY option tuins off all potential
eneigy teims except foi this one.

G#"J'8($#" a+*;Bb Sets the scale factoi neeueu to conveit the eneigy value computeu by the pi-
oibital toisional angle potential into units of kcalmole. The coiiect value is foice fielu uepenuent
anu typically pioviueu in the heauei of the mastei foice fielu paiametei file. The uefault value of 1.u
is useu, if the PIT0RS0NIT keywoiu is not given in the foice fielu paiametei file oi the keyfile.

GO&`-'#I aL /34*X*+)b This keywoiu sets the uimensions of the chaige giiu useu uuiing paiticle
mesh Ewalu summation. The thiee mouifieis give the size along the X-, Y- anu Z-axes, iespectively. If
eithei the Y- oi Z-axis uimensions aie omitteu, then they aie set equal to the X-axis uimension. The
uefault in the absence of the PNE-uRIB keywoiu is to set the giiu size along each axis to the smallest
powei of 2, S anuoi S which is at least as laige as 1.S times the axis length in Angstoms. Note that
the FFT useu by PNE is not iestiicteu to, but is most efficient foi, giiu sizes which aie poweis of 2, S
anuoi S.

GO&`J'I&' a/34*X*+b This keywoiu sets the oiuei of the B-spline inteipolation useu uuiing
paiticle mesh Ewalu summation. A uefault value of 8 is useu in the absence of the PNE-0RBER
keywoiu.

51 "#$%&' ()*+,) -./0* 51
GJPN'`1D`8?NP& a+*;Bb This keywoiu pioviues a multiplicative scale factoi that is applieu to
polaiization inteiactions between 1-2 polaiization gioups, &$!$, paiis of atoms that aie in uiiectly
connecteu polaiization gioups. The uefault value of u.u is useu, if the P0LAR-12-SCALE keywoiu is
not given in eithei the paiametei file oi the keyfile.

GJPN'`1L`8?NP& a+*;Bb This keywoiu pioviues a multiplicative scale factoi that is applieu to
polaiization inteiactions between 1-S polaiization gioups, &$!$, paiis of atoms that aie in polaiization
gioups sepaiateu by one othei gioup. The uefault value of u.u is useu, if the P0LAR-1S-SCALE
keywoiu is not given in eithei the paiametei file oi the keyfile.

GJPN'`1W`8?NP& a+*;Bb This keywoiu pioviues a multiplicative scale factoi that is applieu to
polaiization inteiactions between 1-4 polaiization gioups, &$!$, paiis of atoms that aie in polaiization
gioups sepaiateu by two othei gioups. The uefault value of 1.u is useu, if the P0LAR-14-SCALE
keywoiu is not given in eithei the paiametei file oi the keyfile.

GJPN'`1[`8?NP& a+*;Bb This keywoiu pioviues a multiplicative scale factoi that is applieu to
polaiization inteiactions between 1-S polaiization gioups, &$!$, paiis of atoms that aie in polaiization
gioups sepaiateu by thiee othei gioups. The uefault value of 1.u is useu, if the P0LAR-1S-SCALE
keywoiu is not given in eithei the paiametei file oi the keyfile.

GJPN'`INOG aD +*;B)b Contiols the stiength of the uamping function applieu to inuuceu uipoles
anu uipole polaiization inteiaction eneigies. The fiist mouifiei sets the iauius in Angstoms of a
hypothetical atom with unit polaiizability, while the seconu mouifiei sets the scale factoi foi the
exponent of the uamping function. The uefault values foi the iauius anu the scale factoi aie 1.662
anu 1.u, iespectively. Bamping is eliminateu entiiely by using this keywoiu to set the iauius value to
zeio.

GJPN'`&G8 a+*;Bb This keywoiu sets the conveigence ciiteiion applieu uuiing computation of
self-consistent inuuceu uipoles. The calculation is ueemeu to have conveigeu when the *+, change
(in Bebyes) of the inuuceu uipoles at all polaiizable sites is less than the value specifieu with this
keywoiu. The uefault value in the absence of the keywoiu is 1u
-6
Bebyes.

GJPN'`8J' a+*;Bb Sets a successive oveiielaxation (S0R) factoi foi use in computation of inuuceu
atomic uipoles. 0ptimal values foi this keywoiu will speeu the inuuceu uipole calculation, anu pooi
values can iesult in conveigence failuie. The uefault value in the absence of the P0LAR-S0R keywoiu
is u.7 which often a ieasonable value when shoit-iange intiamoleculai polaiization is piesent. Foi
mouels lacking intiamoleculai polaiization, keywoiu values closei to 1.u may be optimal.

GJPN'#SN"#J$ aI#'&?"cO("(NPb Selects between the use of uiiect anu mutual uipole
polaiization foi foice fielus that incoipoiate the polaiization teim. The BIRECT mouifiei avoius an
iteiative calculation by using only the peimanent electiic fielu in computation of inuuceu uipoles.
The N0T0AL option, which is the uefault in the absence of the P0LARIZATI0N keywoiu, iteiates the
inuuceu uipoles to self-consistency.

GJPN'#S& a1 /34*X*+U 1 +*;B M .@ 45 W /34*X*+)b This keywoiu pioviues the values foi a single
atomic uipole polaiizability paiametei. The integei mouifiei, if positive, gives the atom type numbei
foi which a polaiizability paiametei is to be uefineu. If the fiist integei mouifiei is negative, then the
paiametei value to follow applies only to the inuiviuual atom whose atom numbei is the negative of
the mouifiei. The ieal numbei mouifiei gives the value of the uipole polaiizability in -
S
. The final
integei mouifieis list the atom type numbeis of atoms uiiectly bonueu to the cuiient atom anu which
will be consiueieu to be pait of the cuiient atom's polaiization gioup.
52 "#$%&' ()*+,) -./0* 52

GJPN'#S&"&'O a$J$&cJ$PRb This keywoiu contiols use of the atomic uipole polaiization
potential eneigy teim. In the absence of a mouifying option, this keywoiu tuins on use of the
potential. The N0NE option tuins off use of this potential eneigy teim. The 0NLY option tuins off all
potential eneigy teims except foi this one.

GJPRO&'`?("J>> a+*;Bb Sets the value of an auuitional cutoff paiametei neeueu foi infinite
polymei systems. This value must be set to less than half the minimal peiiouic box uimension anu
shoulu be gieatei than the laigest possible inteiatomic uistance that can be subject to scaling oi
exclusion as a local electiostatic oi van uei Waals inteiaction. The uefault in the absence of the
P0LYNER-C0T0FF keywoiu is S.S Angstioms.

G'#$"J(" a/34*X*+b A geneial paiametei foi iteiative pioceuuies such as minimizations that sets
the numbei of iteiations between wiites of status infoimation to the stanuaiu output. The uefault
value in the absence of the keywoiu is 1, &$!$, the calculation status is given eveiy iteiation.

'NI#(8'(P& aN'#"YO&"#?c-&JO&"'#?c?(V#?`O&N$b Sets the functional foim of the iauius
combining iule foi heteioatomic van uei Waals potential eneigy inteiactions. The uefault in the
absence of the RABI0SR0LE keywoiu is to use the aiithmetic mean combining iule to get iauii foi
heteioatomic inteiactions.

'NI#(88#S& a'NI#(8cI#NO&"&'b Beteimines whethei the atom size values given in van uei
Waals paiameteis ieau fiom vBW keywoiu statements aie inteipieteu as atomic iauius oi uiametei
values. The uefault in the absence of the RABI0SSIZE keywoiu is to assume that vuw size paiameteis
aie given as iauius values.

'NI#(8"RG& a'`O#$c8#-ONb Beteimines whethei atom size values given in van uei Waals
paiameteis ieau fiom vBW keywoiu statements aie inteipieteu as potential minimum (R
min
) oi L}-
style sigma ()) values. The uefault in the absence of the RABI0STYPE keywoiu is to assume that vuw
size paiameteis aie given as R
min
values.

'N$IJO8&&I a/34*X*+b Followeu by an integei value, this keywoiu sets the initial seeu value foi
the ianuom numbei geneiatoi useu by TINKER. Setting RANB0NSEEB to the same value as an
eailiei iun will allow exact iepiouuction of the eailiei calculation. (Note that this will not holu acioss
uiffeient machine types.) RANB0NSEEB shoulu be set to a positive integei less than about 2 billion.
In the absence of the RANB0NSEEB keywoiu the seeu is chosen ``ianuomly'' baseu upon the numbei
of seconus that have elapseu in the cuiient uecaue.

'N""P& aVJ$I8cN$-P&8cI#N"JO#?c"'#N"JO#?c<N"&'b Invokes the iattle algoiithm, a
velocity veision of shake, on poitions of a moleculai system uuiing a moleculai uynamic calculation.
The RATTLE keywoiu can be followeu by any of the mouifieis shown, in which case all occuiiences
of the mouifiei species aie constiaineu at iueal values taken fiom the bonu anu angle paiameteis of
the foice fielu in use. In the absence of any mouifiei, RATTLE constiains all bonus to hyuiogen atoms
at iueal bonu lengths.

'N""P&`I#8"N$?& aD /34*X*+)b This keywoiu allows the use of a ``Rattle'' constiaint between
the two atoms whose numbeis aie specifieu on the keywoiu line. If the two atoms aie involveu in a
covalent bonu, then theii uistance is constiaineu to the iueal bonu length fiom the foice fielu. Foi
nonbonueu atoms, the iattle constiaint is fixeu at theii uistance in the input cooiuinate file.

'N""P&`P#$& a/34*X*+b This keywoiu
53 "#$%&' ()*+,) -./0* 53

'N""P&`J'#-#$ a/34*X*+b This keywoiu

'N""P&`GPN$& a/34*X*+b This keywoiu

'&N?"#J$>#&PI aD +*;B) M 1 /34*X*+b This keywoiu pioviues paiameteis neeueu foi the
ieaction fielu potential eneigy calculation. The two ieal mouifieis give the iauius of the uielectiic
cavity anu the iatio of the bulk uielectiic outsiue the cavity to that insiue the cavity. The integei
mouifiei gives the numbei of teims in the ieaction fielu summation to be useu. In the absence of the
REACTI0NFIELB keywoiu, the uefault values aie a cavity of iauius 1uuuuuu -, a uielectiic iatio of 8u
anu use of only the fiist teim of the ieaction fielu summation.

'&I(?& a+*;Bb Specifies the fiaction between zeio anu one by which the path between staiting
anu final confoimational state will be shoiteneu at each majoi cycle of the tiansition state location
algoiithm implementeu by the SABBLE piogiam. This causes the path enupoints to move up anu out
of the teiminal stiuctuies towaiu the tiansition state iegion. In favoiable cases, a nonzeio value of
the REB0CE mouifiei can speeu conveigence to the tiansition state. The uefault value in the absence
of the REB0CE keywoiu is zeio.

'&8"'N#$`N$-P& aL /34*X*+) M L +*;B)b This keywoiu implements a flat-welleu haimonic
potential that can be useu to iestiain the angle between thiee atoms to lie within a specifieu angle
iange. The integei mouifieis contain the atom numbeis of the thiee atoms whose angle is to be
iestiaineu. The fiist ieal mouifiei is the foice constant in kcaluegiee
2
foi the iestiaint. The last two
ieal mouifieis give the lowei anu uppei bounus in uegiees on the alloweu angle values. If the angle
lies between the lowei anu uppei bounus, the iestiaint potential is zeio. 0utsiue the bounus, the
haimonic iestiaint is applieu. If the angle iange mouifieis aie omitteu, then the atoms aie iestiaineu
to the angle founu in the input stiuctuie. If the foice constant is also omitteu, a uefault value of 1u.u is
useu.

'&8"'N#$`I#8"N$?& aD /34*X*+) M L +*;B)b This keywoiu implements a flat-welleu haimonic
potential that can be useu to iestiain two atoms to lie within a specifieu uistance iange. The integei
mouifieis contain the atom numbeis of the two atoms to be iestiaineu. The fiist ieal mouifiei
specifies the foice constant in kcal-
2
foi the iestiaint. The next two ieal mouifieis give the lowei
anu uppei bounus in -ngstioms on the alloweu uistance iange. If the inteiatomic uistance lies
between these lowei anu uppei bounus, the iestiaint potential is zeio. 0utsiue the bounus, the
haimonic iestiaint is applieu. If the uistance iange mouifieis aie omitteu, then the atoms aie
iestiaineu to the inteiatomic uistance founu in the input stiuctuie. If the foice constant is also
omitteu, a uefault value of 1uu.u is useu.

'&8"'N#$`-'J(G8 aD /34*X*+) M L +*;B)b This keywoiu implements a flat-welleu haimonic
uistance iestiaint between the centeis-of-mass of two gioups of atoms. The integei mouifieis aie the
numbeis of the two gioups which must be uefineu sepaiately via the uR00P keywoiu. The fiist ieal
mouifiei is the foice constant in kcal-
2
foi the iestiaint. The last two ieal mouifieis give the lowei
anu uppei bounus in -ngstioms on the alloweu inteigioup centei-of-mass uistance values. If the
uistance iange mouifieis aie omitteu, then the gioups aie iestiaineu to the uistance founu in the
input stiuctuie. If the foice constant is also omitteu, a uefault value of 1uu.u is useu.

'&8"'N#$`GJ8#"#J$ a1 /34*X*+ M [ +*;B)b This keywoiu pioviues the ability to iestiain an
inuiviuual atom to a specifieu cooiuinate position. The initial integei mouifiei contains the atom
numbei of the atom to be iestiaineu. The fiist ieal mouifiei sets the foice constant in kcal-
2
foi the
haimonic iestiaint potential. The next thiee ieal numbei mouifieis give the X-, Y- anu Z-cooiuinates
54 "#$%&' ()*+,) -./0* 54
to which the atom is tetheieu. The final ieal mouifiei uefines a spheie aiounu the specifieu
cooiuinates within which the iestiaint value is zeio. If the exclusion spheie iauius is omitteu, it is
taken to be zeio. If the cooiuinates aie omitteu, then the atom is iestiaineu to the oiigin. If the foice
constant is also omitteu, a uefault value of 1uu.u is useu.

'&8"'N#$`"J'8#J$ aW /34*X*+) M L +*;B)b This keywoiu implements a flat-welleu haimonic
potential that can be useu to iestiain the toisional angle between foui atoms to lie within a specifieu
angle iange. The initial integei mouifieis contains the atom numbeis of the foui atoms whose
toisional angle, computeu in the atom oiuei listeu, is to be iestiaineu. The fiist ieal mouifiei gives a
foice constant in kcaluegiee
2
foi the iestiaint. The last two ieal mouifieis give the lowei anu uppei
bounus in uegiees on the alloweu toisional angle values. The angle values given can wiap aiounu
acioss -18u anu +18u uegiees. 0utsiue the alloweu angle iange, the haimonic iestiaint is applieu. If
the angle iange mouifieis aie omitteu, then the atoms aie iestiaineu to the toisional angle founu in
the input stiuctuie. If the foice constant is also omitteu, a uefault value of 1.u is useu.

'&8"'N#$"&'O a$J$&cJ$PRb This keywoiu contiols use of the iestiaint potential eneigy
teims. In the absence of a mouifying option, this keywoiu tuins on use of these potentials. The N0NE
option tuins off use of these potential eneigy teims. The 0NLY option tuins off all potential eneigy
teims except foi these teims.

'Q$>#&PI"&'O a$J$&cJ$PRb This keywoiu contiols use of the ieaction fielu continuum
solvation potential eneigy teim. In the absence of a mouifying option, this keywoiu tuins on use of
the potential. The N0NE option tuins off use of this potential eneigy teim. The 0NLY option tuins off
all potential eneigy teims except foi this one.

8NIIP&GJ#$" The piesence of this keywoiu allows Newton-style seconu ueiivative-baseu
optimization ioutine useu by NEWT0N, NEWTR0T anu othei piogiams to conveige to sauulepoints
as well as minima on the potential suiface. By uefault, in the absence of the SABBLEP0INT keywoiu,
checks aie applieu that pievent conveigence to stationaiy points having uiiections of negative
cuivatuie.

8NZ&`?R?P& This keywoiu causes TINKER piogiams, such as minimizations, that output
inteimeuiate cooiuinate sets to save each successive set to the next consecutively numbeieu cycle
file. The SAvE-CYCLE keywoiu is the opposite of the 0vERWRITE keywoiu.

8NZ&`>J'?& This keywoiu causes TINKER moleculai uynamics calculations to save the values of
the foice components on each atom to a sepaiate cycle file. These files aie wiitten whenevei the
atomic cooiuinate snapshots aie wiitten uuiing the uynamics iun. Each atomic foice file name
contains as a suffix the cycle numbei followeu by the lettei f.

8NZ&`#$I(?&I This keywoiu causes TINKER moleculai uynamics calculations that involve
polaiizable atomic multipoles to save the values of the inuuceu uipole components on each
polaiizable atom to a sepaiate cycle file. These files aie wiitten whenevei the atomic cooiuinate
snapshots aie wiitten uuiing the uynamics iun. Each inuuceu uipole file name contains as a suffix the
cycle numbei followeu by the lettei u.

8NZ&`Z&PJ?#"R This keywoiu causes TINKER moleculai uynamics calculations to save the values
of the velocity components on each atom to a sepaiate cycle file. These files aie wiitten whenevei the
atomic cooiuinate snapshots aie wiitten uuiing the uynamics iun. Each velocity file name contains
as a suffix the cycle numbei followeu by the lettei v.

55 "#$%&' ()*+,) -./0* 55
8PJG&ONQ a+*;Bb This keywoiu anu its mouifying value set the maximum alloweu size of the iatio
between the cuiient anu initial piojecteu giauients uuiing the line seaich phase of conjugate
giauient oi tiuncateu Newton optimizations. If this iatio exceeus SL0PENAX, then the initial step
size is ieuuceu by a factoi of 1u. The uefault value is usually set to 1uuuu.u when not specifieu via the
SL0PENAX keywoiu.

8OJJ"Y#$- aI&Oc-INc"JGYN"c8"JGYN"b This keywoiu activates the potential eneigy
smoothing methous. Seveial vaiiations aie available uepenuing on the value of the mouifiei useu:
BEN= Biffusion Equation Nethou with a stanuaiu uaussian keinel; uBA= uaussian Bensity
Annealing as pioposeu by the Stiaub gioup; T0PBAT= a local BEN-like methou using a finite iange
``tophat'' keinel; ST0PBAT= shifteu tophat smoothing.

8JPZN"& aN8Gc8N8NcJ$#J$c8"#PPcY?"cN?&c-V8Nb 0se of this keywoiu uuiing eneigy
calculations with any of the stanuaiu foice fielus tuins on a continuum solvation fiee eneigy teim.
Seveial algoiithms aie available baseu on the mouifiei useu: ASP= Eisenbeig-NcLachlan ASP methou
using the Wesson-Eisenbeig vacuum-to-watei paiameteis; SASA= the 0oi-Scheiaga SASA methou;
0NI0N= the oiiginal 199u Still ``0nion-shell'' uBSA methou; STILL= the 1997 analytical uBSA
methou fiom Still's gioup; BCT= the paiiwise uescieening methou of Bawkins, Ciamei anu Tiuhlai;
ACE= the Analytical Continuum Electiostatics solvation methou fiom the Kaiplus gioup; uBSA=
equivalent to the STILL mouifiei. At piesent, uBSA-style methous aie only valiu foi foice fielus that
use simple paitial chaige electiostatics.

8JPZN"&"&'O a$J$&cJ$PRb This keywoiu contiols use of the macioscopic solvation potential
eneigy teim. In the absence of a mouifying option, this keywoiu tuins on use of the potential. The
N0NE option tuins off use of this potential eneigy teim. The 0NLY option tuins off all potential
eneigy teims except foi this one.

8GN?&-'J(G a3;C*b This keywoiu selects the space gioup to be useu in manipulation of ciystal
unit cells anu asymmetiic units. The name option must be chosen fiom one of the following cuiiently
implementeu space gioups: P1, P1(-), P21, Cc, P21a, P21n, P21c, C2c, P212121, Pna21, Pn21a,
Cmc21, Pccn, Pbcn, Pbca, P41, I41a, P4(-)21c, P4(-)m2, RSc, P6(S)mcm, FmS(-)m, ImS(-)m.

8GY&'& aW +*;B)U 5+ 1 /34*X*+ M 1 +*;Bb This keywoiu pioviues an alteinative to the ACTIvE anu
INACTIvE keywoius foi specification of subsets of active atoms. If foui ieal numbei mouifieis aie
pioviueu, the fiist thiee aie taken as X-, Y- anu Z-cooiuinates anu the fouith is the iauius of a spheie
centeieu at these cooiuinates. In this case, all atoms within the spheie at the ,"(*" of the calculation
aie active "8*45/845" the calculation, while all othei atoms aie inactive. Similaily if one integei anu
ieal numbei aie given, an ``active'' spheie with iauius set by the ieal is centeieu on the system atom
with atom numbei given by the integei mouifiei. Nultiple SPBERE keywoiu lines can be piesent in a
single keyfile, anu the list of active atoms specifieu by the spheies is cumulative.

8"&&G&8"`I&8?&$" This keywoiu foices the L-BFuS optimization ioutine useu by the NININIZE
piogiam anu othei piogiams to peifoim steepest uescent minimization. This option can be useful in
conjunction with small step sizes foi following minimum eneigy paths, but is geneially infeiioi to the
L-BFuS uefault foi most optimization puiposes.

8"&GONQ a+*;Bb This keywoiu anu its mouifying value set the maximum size of an inuiviuual step
uuiing the line seaich phase of conjugate giauient oi tiuncateu Newton optimizations. The step size
is computeu as the noim of the vectoi of changes in paiameteis being optimizeu. The uefault value
uepenus on the paiticulai TINKER piogiam, but is usually in the iange fiom 1.u to S.u when not
specifieu via the STEPNAX keywoiu.

56 "#$%&' ()*+,) -./0* 56
8"&GO#$ a+*;Bb This keywoiu anu its mouifying value set the minimum size of an inuiviuual step
uuiing the line seaich phase of conjugate giauient oi tiuncateu Newton optimizations. The step size
is computeu as the noim of the vectoi of changes in paiameteis being optimizeu. The uefault value is
usually set to about 1u
-16
when not specifieu via the STEPNIN keywoiu.

8"'V$I a1 /34*X*+ M L +*;B)b This keywoiu pioviues the values foi a single stietch-benu cioss
teim potential paiametei. The integei mouifiei gives the atom class numbei foi the cential atom of
the bonu angle involveu in stietch-benu inteiactions. The ieal numbei mouifieis give the foice
constant values to be useu when the cential atom of the angle is attacheu to u, 1 oi 2 auuitional
hyuiogen atoms, iespectively. The uefault units foi the stietch-benu foice constant aie kcalmole--
uegiee, but this can be contiolleu via the STRBNB0NIT keywoiu.

8"'V$I"&'O a$J$&cJ$PRb This keywoiu contiols use of the bonu stietching-angle benuing
cioss teim potential eneigy. In the absence of a mouifying option, this keywoiu tuins on use of the
potential. The N0NE option tuins off use of this potential eneigy teim. The 0NLY option tuins off all
potential eneigy teims except foi this one.

8"'V$I($#" a+*;Bb Sets the scale factoi neeueu to conveit the eneigy value computeu by the
bonu stietching-angle benuing cioss teim potential into units of kcalmole. The coiiect value is foice
fielu uepenuent anu typically pioviueu in the heauei of the mastei foice fielu paiametei file. The
uefault value of 1.u is useu, if the STRBNB0NIT keywoiu is not given in the foice fielu paiametei file
oi the keyfile.

8"'"J'8 aD /34*X*+) M 1 +*;Bb This keywoiu pioviues the values foi a single stietch-toision
cioss teim potential paiametei. The two integei mouifieis give the atom class numbeis foi the atoms
involveu in the cential bonu of the toisional angles to be paiameteiizeu. The ieal mouifiei gives the
value of the stietch-toision foice constant foi all toisional angles with the uefineu cential bonu atom
classes. The uefault units foi the stietch-toision foice constant can be contiolleu via the
STRT0R0NIT keywoiu.

8"'"J'"&'O a$J$&cJ$PRb This keywoiu contiols use of the bonu stietching-toisional angle
cioss teim potential eneigy. In the absence of a mouifying option, this keywoiu tuins on use of the
potential. The N0NE option tuins off use of this potential eneigy teim. The 0NLY option tuins off all
potential eneigy teims except foi this one.

8"'"J'($#" a+*;Bb Sets the scale factoi neeueu to conveit the eneigy value computeu by the
bonu stietching-toisional angle cioss teim potential into units of kcalmole. The coiiect value is
foice fielu uepenuent anu typically pioviueu in the heauei of the mastei foice fielu paiametei file.
The uefault value of 1.u is useu, if the STRT0R0NIT keywoiu is not given in the foice fielu paiametei
file oi the keyfile.

"NG&' a+*;Bb This keywoiu allows mouification of the cutoff winuows foi nonbonueu potential
eneigy inteiactions. The nonbonueu teims aie smoothly ieuuceu fiom theii stanuaiu value at the
beginning of the cutoff winuow to zeio at the fai enu of the winuow. The fai enu of the winuow is
specifieu via the C0T0FF keywoiu oi its potential function specific vaiiants. The mouifiei value
supplieu with the TAPER keywoiu sets the beginning of the cutoff winuow. The mouifiei can be given
eithei as an absolute uistance value in Angstioms, oi as a fiaction between zeio anu one of the
C0T0FF uistance. The uefault value in the absence of the TAPER keywoiu ianges fiom u.6S to u.9 of
the C0T0FF uistance uepenuing on the type of potential function. The winuows aie implementeu via
polynomial-baseu switching functions, in some cases combineu with eneigy shifting.

57 "#$%&' ()*+,) -./0* 57
"N(`G'&88('& a+*;Bb Sets the coupling time in picoseconus foi the uioningen-style piessuie bath
coupling useu to contiol the system piessuie uuiing moleculai uynamics calculations. A uefault value
of 2.u is useu foi TA0-PRESS0RE in the absence of the keywoiu.

"N(`"&OG&'N"('& a+*;Bb Sets the coupling time in picoseconus foi the uioningen-style
tempeiatuie bath coupling useu to contiol the system tempeiatuie uuiing moleculai uynamics
calculations. A uefault value of u.1 is useu foi TA0-TENPERAT0RE in the absence of the keywoiu.

"Y&'OJ8"N" aV&'&$I8&$cN$I&'8&$b This keywoiu selects a theimostat algoiithm foi use
uuiing moleculai uynamics. Two mouifieis aie available, a Beienusen bath coupling methou, anu an
Anueisen stochastic collision methou. The uefault in the absence of the TBERN0STAT keywoiu is to
use the BERENBSEN algoiithm.

"J'8#J$ aW /34*X*+) M .@ 45 ] +*;Bc+*;Bc/34*X*+ 4+/@B*)b This keywoiu pioviues the values foi
a single toisional angle paiametei. The fiist foui integei mouifieis give the atom class numbeis foi
the atoms involveu in the toisional angle to be uefineu. Each of the iemaining tiiples of
iealiealintegei mouifieis give the amplituue, phase offset in uegiees anu peiiouicity of a paiticulai
toisional function teim, iespectively. Peiiouicities thiough 6-folu aie alloweu foi toisional
paiameteis.

"J'8#J$W aW /34*X*+) M .@ 45 ] +*;Bc+*;Bc/34*X*+ 4+/@B*)b This keywoiu pioviues the values foi
a single toisional angle paiametei specific to atoms in 4-membeieu iings. The fiist foui integei
mouifieis give the atom class numbeis foi the atoms involveu in the toisional angle to be uefineu.
The iemaining tiiples of ieal numbei anu integei mouifieis opeiate as uesciibeu above foi the
T0RSI0N keywoiu.

"J'8#J$[ aW /34*X*+) M .@ 45 ] +*;Bc+*;Bc/34*X*+ 4+/@B*)b This keywoiu pioviues the values foi
a single toisional angle paiametei specific to atoms in S-membeieu iings. The fiist foui integei
mouifieis give the atom class numbeis foi the atoms involveu in the toisional angle to be uefineu.
The iemaining tiiples of ieal numbei anu integei mouifieis opeiate as uesciibeu above foi the
T0RSI0N keywoiu.

"J'8#J$"&'O a$J$&cJ$PRb This keywoiu contiols use of the toisional angle potential eneigy
teim. In the absence of a mouifying option, this keywoiu tuins on use of the potential. The N0NE
option tuins off use of this potential eneigy teim. The 0NLY option tuins off all potential eneigy
teims except foi this one.

"J'8#J$($#" a+*;Bb Sets the scale factoi neeueu to conveit the eneigy value computeu by the
toisional angle potential into units of kcalmole. The coiiect value is foice fielu uepenuent anu
typically pioviueu in the heauei of the mastei foice fielu paiametei file. The uefault value of 1.u is
useu, if the T0RSI0N0NIT keywoiu is not given in the foice fielu paiametei file oi the keyfile.

"J'"J' a_ /34*X*+)U 47*3 C.B4/@B* B/3*) 59 D /34*X*+) ;30 1 +*;Bb This keywoiu is useu to
pioviue the values foi a single toision-toision paiametei. The fiist five integei mouifieis give the
atom class numbeis foi the atoms involveu in the two aujacent toisional angles to be uefineu. The
last two integei mouifieis contain the numbei of uata giiu points that lie along each axis of the
toision-toision map. Foi example, this value will be 1S foi a Su uegiee toisional angle spacing, &$!$,
S6uSu = 12, but 1S values aie iequiieu since uata values foi -18u anu +18u uegiees must both be
supplieu. The subsequent lines contain the toision-toision map uata as the integei values in uegiees
of each toisional angle anu the taiget eneigy value in kcalmole.

58 "#$%&' ()*+,) -./0* 58
"J'"J'"&'O a$J$&cJ$PRb This keywoiu contiols use of the toision-toision potential eneigy
teim. In the absence of a mouifying option, this keywoiu tuins on use of the potential. The N0NE
option tuins off use of this potential eneigy teim. The 0NLY option tuins off all potential eneigy
teims except foi this one.

"J'"J'($#" a+*;Bb Sets the scale factoi neeueu to conveit the eneigy value computeu by the
toision-toision potential into units of kcalmole. The coiiect value is foice fielu uepenuent anu
typically pioviueu in the heauei of the mastei foice fielu paiametei file. The uefault value of 1.u is
useu, if the T0RT0R0NIT keywoiu is not given in the foice fielu paiametei file oi the keyfile.

"'#NP`I#8"N$?& a?PN88#?c'N$IJOc"'#?J'cYNZ&P /34*X*+cGN#'<#8& /34*X*+b Sets
the methou foi selection of a tiial uistance matiix uuiing uistance geometiy computations. The
keywoiu takes a mouifiei that selects the methou to be useu. The BAvEL anu PAIRWISE mouifieis
also iequiie an auuitional integei value that specifies the numbei of atoms useu in metiization anu
the peicentage of metiization, iespectively. The uefault in the absence of this keywoiu is to use the
PAIRWISE methou with 1uu peicent metiization. Fuithei infoimation on the vaiious methous is
given with the uesciiption of the TINKER uistance geometiy piogiam.

"'#NP`I#8"'#V("#J$ a+*;Bb Sets the initial value foi the mean of the uaussian uistiibution useu
to select tiial uistances between the lowei anu uppei bounus uuiing uistance geometiy
computations. The value given must be between u anu 1 which iepiesent the lowei anu uppei
bounus iespectively. This keywoiu is iaiely neeueu since TINKER will usually be able to choose a
ieasonable value by uefault.

"'($?N"& Causes all uistance-baseu nonbonu eneigy cutoffs to be shaiply tiuncateu to an eneigy
of zeio at uistances gieatei than the value set by the cutoff keywoiu(s) without use of any shifting,
switching oi smoothing schemes. At all uistances within the cutoff spheie, the full inteiaction eneigy
is computeu.

('&R`?(V#? a+*;Bb Sets the value of the cubic teim in the Tayloi seiies expansion foim of the
0iey-Biauley potential eneigy. The ieal numbei mouifiei gives the value of the coefficient as a
multiple of the quauiatic coefficient. The uefault value in the absence of the 0REY-C0BIC keywoiu is
zeio; &$!$, the cubic 0iey-Biauley teim is omitteu.

('&R`K(N'"#? a+*;Bb Sets the value of the quaitic teim in the Tayloi seiies expansion foim of the
0iey-Biauley potential eneigy. The ieal numbei mouifiei gives the value of the coefficient as a
multiple of the quauiatic coefficient. The uefault value in the absence of the 0REY-Q0ARTIC keywoiu
is zeio; &$!$, the quaitic 0iey-Biauley teim is omitteu.

('&RV'NI aL /34*X*+) M D +*;B)b This keywoiu pioviues the values foi a single 0iey-Biauley
cioss teim potential paiametei. The integei mouifieis give the atom class numbeis foi the thiee
kinus of atoms involveu in the angle foi which a 0iey-Biauley teim is to be uefineu. The ieal numbei
mouifieis give the foice constant value foi the teim anu the taiget value foi the 1-S uistance in -. The
uefault units foi the foice constant aie kcalmole-
2
, but this can be contiolleu via the 0REY0NIT
keywoiu.

('&R"&'O a$J$&cJ$PRb This keywoiu contiols use of the 0iey-Biauley potential eneigy teim.
In the absence of a mouifying option, this keywoiu tuins on use of the potential. The N0NE option
tuins off use of this potential eneigy teim. The 0NLY option tuins off all potential eneigy teims
except foi this one.

59 "#$%&' ()*+,) -./0* 59
('&R($#" a+*;Bb Sets the scale factoi neeueu to conveit the eneigy value computeu by the 0iey-
Biauley potential into units of kcalmole. The coiiect value is foice fielu uepenuent anu typically
pioviueu in the heauei of the mastei foice fielu paiametei file. The uefault value of 1.u is useu, if the
0REY0NIT keywoiu is not given in the foice fielu paiametei file oi the keyfile.

ZI< a1 /34*X*+ M L +*;B)b This keywoiu pioviues values foi a single van uei Waals paiametei.
The integei mouifiei, if positive, gives the atom class numbei foi which vuw paiameteis aie to be
uefineu. Note that vuw paiameteis aie given foi atom classes, not atom types. The thiee ieal numbei
mouifieis give the values of the atom size in -, homoatomic well uepth in kcalmole, anu an optional
ieuuction factoi foi univalent atoms.

ZI<`1D`8?NP& a+*;Bb This keywoiu pioviues a multiplicative scale factoi that is applieu to van
uei Waals potential inteiactions between 1-2 connecteu atoms, &$!$, atoms that aie uiiectly bonueu.
The uefault value of u.u is useu, if the vBW-12-SCALE keywoiu is not given in eithei the paiametei
file oi the keyfile.

ZI<`1L`8?NP& a+*;Bb This keywoiu pioviues a multiplicative scale factoi that is applieu to van
uei Waals potential inteiactions between 1-S connecteu atoms, &$!$, atoms sepaiateu by two covalent
bonus. The uefault value of u.u is useu, if the vBW-1S-SCALE keywoiu is not given in eithei the
paiametei file oi the keyfile.

ZI<`1W`8?NP& a+*;Bb This keywoiu pioviues a multiplicative scale factoi that is applieu to van
uei Waals potential inteiactions between 1-4 connecteu atoms, &$!$, atoms sepaiateu by thiee
covalent bonus. The uefault value of 1.u is useu, if the vBW-14-SCALE keywoiu is not given in eithei
the paiametei file oi the keyfile.

ZI<`1[`8?NP& a+*;Bb This keywoiu pioviues a multiplicative scale factoi that is applieu to van
uei Waals potential inteiactions between 1-S connecteu atoms, &$!$, atoms sepaiateu by foui covalent
bonus. The uefault value of 1.u is useu, if the vBW-1S-SCALE keywoiu is not given in eithei the
paiametei file oi the keyfile.

ZI<`?("J>> a+*;Bb Sets the cutoff uistance value in Angstioms foi van uei Waals potential
eneigy inteiactions. The eneigy foi any paii of van uei Waals sites beyonu the cutoff uistance will be
set to zeio. 0thei keywoius can be useu to select a smoothing scheme neai the cutoff uistance. The
uefault cutoff uistance in the absence of the vBW-C0T0FF keywoiu is infinite foi nonpeiiouic
systems anu 9.u foi peiiouic systems.

ZI<`"NG&' a+*;Bb This keywoiu allows mouification of the cutoff winuows foi van uei Waals
potential eneigy inteiactions. It is similai in foim anu action to the TAPER keywoiu, except that its
value applies only to the vuw potential. The uefault value in the absence of the vBW-TAPER keywoiu
is to begin the cutoff winuow at u.9 of the vuw cutoff uistance.

ZI<1W a1 /34*X*+ M D +*;B)b This keywoiu pioviues values foi a single van uei Waals paiametei
foi use in 1-4 nonbonueu inteiactions. The integei mouifiei, if positive, gives the atom class numbei
foi which vuw paiameteis aie to be uefineu. Note that vuw paiameteis aie given foi atom classes,
not atom types. The two ieal numbei mouifieis give the values of the atom size in - anu the
homoatomic well uepth in kcalmole. Reuuction factois, if useu, aie caiiieu ovei fiom the vBW
keywoiu foi the same atom class.

ZI<G' aD /34*X*+) M D +*;B)b This keywoiu pioviues the values foi the vuw paiameteis foi a
single special heteioatomic paii of atoms. The integei mouifieis give the paii of atom class numbeis
60 "#$%&' ()*+,) -./0* 60
foi which special vuw paiameteis aie to be uefineu. The two ieal numbei mouifieis give the values of
the minimum eneigy contact uistance in - anu the well uepth at the minimum uistance in kcalmole.

ZI<"&'O a$J$&cJ$PRb This keywoiu contiols use of the van uei Waals iepulsion-uispeision
potential eneigy teim. In the absence of a mouifying option, this keywoiu tuins on use of the
potential. The N0NE option tuins off use of this potential eneigy teim. The 0NLY option tuins off all
potential eneigy teims except foi this one.

ZI<"RG& aP&$$N'I`eJ$&8 c V(?%#$-YNO c V(>>&'&I`1W`_ c OOL`YVJ$I c -N(88#N$b
Sets the functional foim foi the van uei Waals potential eneigy teim. The text mouifiei gives the
name of the functional foim to be useu. The uA0SSIAN mouifiei value implements a two oi foui
uaussian fit to the coiiesponuing Lennaiu-}ones function foi use with potential eneigy smoothing
schemes. The uefault in the absence of the vBWTYPE keywoiu is to use the stanuaiu two paiametei
Lennaiu-}ones function.

Z&'VJ8& Tuins on piinting of seconuaiy anu infoimational output uuiing a vaiiety of TINKER
computations; a subset of the moie extensive output pioviueu by the BEB0u keywoiu.

<NPP a+*;Bb Sets the iauius of a spheiical bounuaiy useu to maintain uioplet bounuaiy
conuitions. The ieal mouifiei specifies the uesiieu appioximate iauius of the uioplet. In piactice, an
aitificial van uei Waals wall is constiucteu at a fixeu buffei uistance of 2.S - outsiue the specifieu
iauius. The effect is that atoms which attempt to move outsiue the iegion uefineu by the uioplet
iauius will be foiceu towaiu the centei.

<'#"&J(" a/34*X*+b A geneial paiametei foi iteiative pioceuuies such as minimizations that
sets the numbei of iteiations between wiites of inteimeuiate iesults (such as the cuiient
cooiuinates) to uisk file(s). The uefault value in the absence of the keywoiu is 1, &$!$, the inteimeuiate
iesults aie wiitten to file on eveiy iteiation. Whethei successive inteimeuiate iesults aie saveu to
new files oi ieplace pieviously wiitten inteimeuiate iesults is contiolleu by the 0vERWRITE anu
SAvE-CYCLE keywoius.

61 "#$%&' ()*+,) -./0* 61
h2 >5+6* >/*B0 G;+;C*4*+ 8*4)
The TINKER package is uistiibuteu with seveial foice fielu paiametei sets, implementing a selection
of wiuely useu liteiatuie foice fielus as well as the TINKER foice fielu cuiiently unuei constiuction in
the Ponuei lab. We tiy to exactly iepiouuce the intent of the oiiginal authois of oui uistiibuteu,
thiiu-paity foice fielus. In all cases the paiametei sets have been valiuateu against liteiatuie iepoits,
iesults pioviueu by the oiiginal uevelopeis, oi calculations maue with the authentic piogiams. With
the few exceptions noteu below, TINKER calculations can be tieateu as authentic iesults fiom the
genuine foice fielus. A biief uesciiption of each paiametei set, incluuing some still in piepaiation anu
not uistiibuteu with the cuiient veision, is pioviueu below with leau liteiatuie iefeiences foi the
foice fielu:

NOJ&VN2G'O

Paiameteis foi the AN0EBA polaiizable atomic multipole foice fielu. As of the cuiient TINKER
ielease, we have completeu paiametiization foi a numbei of ions anu small oiganic molecules. Foi
fuithei infoimation, oi if you aie inteiesteu in ueveloping oi testing paiameteis foi othei small
molecules, please contact the Ponuei lab.

P. Ren anu }. W. Ponuei, A Consistent Tieatment of Intei- anu Intiamoleculai Polaiization in
Noleculai Nechanics Calculations, BA C)D49*A C-+DA, <=, 1497-1Su6 (2uu2)

P. Ren anu }. W. Ponuei, Polaiizable Atomic Nultipole Watei Nouel foi Noleculai Nechanics
Simulation, BA E-0"A C-+DA F, >?@, S9SS-S947 (2uuS)

P. Ren anu }. W. Ponuei, Ion Solvation Theimouynamics fiom Simulation with a Polaiizable Foice
Fielu, A. uiossfielu, BA GDA C-+DA H)6A, ><A, 1S671-1S682 (2uuS)

NOJ&VNG'J2G'O

Pieliminaiy piotein paiameteis foi the AN0EBA polaiizable atomic multipole foice fielu. While the
uistiibuteu paiameteis aie still subject to minoi alteiation as we continue valiuation, they aie now
stable enough foi othei gioups to begin using them. Foi fuithei infoimation, oi if you aie inteiesteu
in testing the piotein paiametei set, please contact the Ponuei lab.

}. W. Ponuei anu B. A. Case, Foice Fielus foi Piotein Simulation, G3!A E2)*A C-+DA, BB, 27-8S (2uuS)

P. Ren anu }. W. Ponuei, Polaiizable Atomic Nultipole-baseu Potential foi Pioteins: Nouel anu
Paiameteiization, &. 2*!2(*("&4.

NOV&'iW2G'O

ANBER CCDE paiameteis foi pioteins anu nucleic acius. Note that with theii ``Coinell'' foice fielu, the
Kollman gioup has ueviseu sepaiate, fully inuepenuent paitial chaige values foi each of the N- anu C-
teiminal amino aciu iesiuues. At piesent, the teiminal iesiuue chaiges foi TINKER's veision maintain
the coiiect foimal chaige, but ieuistiibuteu somewhat at the alpha caibon atoms fiom the oiiginal
Kollman gioup values. The total magnituue of the ieuistiibution is less than u.u1 elections in most
cases.

W. B. Coinell, P. Cieplak, C. I. Bayly, I. R. uoulu, K. N. Neiz, }i., B. N. Feiguson, B. C. Spellmeyei, T. Fox,
}. W. Caluwell anu P. A. Kollman, A Seconu ueneiation Foice Fielu foi the Simulation of Pioteins,
Nucleic Acius, anu 0iganic Nolecules, BA GDA C-+DA H)6A, >>@, S179-S197 (199S) |CC94j
62 "#$%&' ()*+,) -./0* 62

u. Noyna, B. }. Williams, R. }. Nachman anu A. I. Scott, Confoimation in Solution anu Bynamics of a
Stiuctuially Constiaineu Lineai Insect Kinin Pentapeptiue Analogue, F.)4)I0D+2", ED, 4uS-41S
(1999) |AIB chaigesj

W. S. Ross anu C. C. Baiuin, Ion-Inuuceu Stabilization of the u-BNA Quauiuplex: Fiee Eneigy
Peituibation Stuuies, BA GDA C-+DA H)6A, >>B, 4S6S-4S66 (1994) |alkali metal ionsj

}. Aqvist, Ion-Watei Inteiaction Potentials Beiiveu fiom Fiee Eneigy Peituibation Simulations, BA
E-0"A C-+DA, DE, 8u21-8u24, 199u |alkaline eaith Ions, iauii auapteu foi Ambei combining iulej

Cuiient foice fielu paiametei values anu suggesteu pioceuuies foi uevelopment of paiameteis foi
auuitional molecules aie available fiom the Ambei web site in the Case lab at Sciipps,
http:ambei.sciipps.euu

NOV&'i]2G'O

ANBER CCDB paiameteis foi pioteins anu nucleic acius. The only change fiom the CCDE paiametei set
is in the toisional paiameteis foi the piotein phipsi angles. These values weie alteieu to give bettei
agieement with changes of CCDB with LNP2 QN iesults fiom the Fiiesnei lab on alanine uipeptiue
anu tetiapeptiue.

P. Kollman, R. Bixon, W. Coinell, T. Fox, C. Chipot anu A. Pohoiille, The Bevelopment Application of a
'Ninimalist' 0iganicBiochemical Noleculai Nechanic Foice Fielu using a Combination of (F G.&"&4
Calculations anu Expeiimental Bata, in ?5C@.4*+ 8/C.B;4/53 59 V/5C5B*6.B;+ 8E)4*C), W. F. van
uunsteien, P. K. Weinei, A. }. Wilkinson, eus., volume S, 8S-96 (1997) |CC96j

Cuiient foice fielu paiametei values anu suggesteu pioceuuies foi uevelopment of paiameteis foi
auuitional molecules aie available fiom the Ambei web site in the Case lab at Sciipps,
http:ambei.sciipps.euu

NOV&'ih2G'O

ANBER CCDH paiameteis foi pioteins anu nucleic acius. The only change fiom the CCDE paiametei set
is in the glycosiuic toisional paiameteis that contiol sugai puckei.

T. E. Cheatham III, P. Cieplak anu P. A. Kollman, A Nouifieu veision of the Coinell et al. Foice Fielu
with Impioveu Sugai Puckei Phases anu Belical Repeat, BA F.)D)IA H*296*A J05A, >B, 84S-862 (1999)

Cuiient foice fielu paiametei values anu suggesteu pioceuuies foi uevelopment of paiameteis foi
auuitional molecules aie available fiom the Ambei web site in the Case lab at Sciipps,
http:ambei.sciipps.euu

NOV&'ii2G'O

ANBER CCDD paiameteis foi pioteins anu nucleic acius. The oiiginal paitial chaiges fiom the CCDE
paiametei set aie ietaineu, but many of the bonu, angle anu toisional paiameteis have been ieviseu
to pioviue bettei geneial agieement with expeiiment.

}. Wang, P. Cieplak anu P. A. Kollman, Bow Well Boes a Restiaineu Electiostatic Potential (RESP)
Nouel Peifoim in Calcluating Confoimational Eneigies of 0iganic anu Biological Nolecules., BA
C)D49*A C-+DA, <>, 1u49-1u74 (2uuu)

63 "#$%&' ()*+,) -./0* 63
Cuiient foice fielu paiametei values anu suggesteu pioceuuies foi uevelopment of paiameteis foi
auuitional molecules aie available fiom the Ambei web site in the Case lab at Sciipps,
http:ambei.sciipps.euu

?YN'OO1i2G'O

CBARNN19 uniteu-atom paiameteis foi pioteins. The nucleic aciu paiametei aie not yet
implementeu. Theie aie some uiffeiences between authentic CBARNN19 anu the TINKER veision
uue to ieplacement of CBARNN impiopeis by toisions foi cases that involve atoms not bonueu to
the tiigonal atom anu TINKER's use of all possible toisions acioss a bonu insteau of a single toision
pei bonu.

E. Neiia, S. Fischei anu N. Kaiplus, Simulation of Activation Fiee Eneigies in Noleculai Systems, BA
C-+DA E-0"A, >?A, 19u2-1921 (1996)

L. Nilsson anu N. Kaiplus, Empiiical Eneigy Functions foi Eneigy Ninimizations anu Bynamics of
Nucleic Acius, BA C)D49*A C-+DA, @, S91-616 (1986)

W. E. Reihei III, Theoietical Stuuies of Byuiogen Bonuing, Ph.B. Thesis, Bepaitment of Chemistiy,
Baivaiu 0niveisity, Cambiiuge, NA, 198S

?YN'OODD2G'O

CBARNN27 all-atom paiameteis foi pioteins anu lipius. Nost of the nucleic aciu anu small mouel
compounu paiameteis aie not yet implementeu. We plan to pioviue these auuitional paiameteis in
uue couise.

N. Foloppe anu A. B. NacKeiell, }i., All-Atom Empiiical Foice Fielu foi Nucleic Acius: 1) Paiametei
0ptimization Baseu on Small Nolecule anu Conuenseu Phase Naciomoleculai Taiget Bata, BA C)D49*A
C-+DA, <>, 86-1u4 (2uuu) |CBARNN27j

N. Banavali anu A. B. NacKeiell, }i., All-Atom Empiiical Foice Fielu foi Nucleic Acius: 2) Application
to Noleculai Bynamics Simulations of BNA anu RNA in Solution, BA C)D49*A C-+DA, <>, 1uS-12u
(2uuu)

A. B. NacKeiiell, }i., !" ()$, All-Atom Empiiical Potential foi Noleculai Noueling anu Bynamics Stuuies
of Pioteins, BA E-0"A C-+DA F, >?<, SS86-S616 (1998) |CBARNN22j

A. B. NacKeiell, }i., }. Wioikeiwicz-Kuczeia anu N. Kaiplus, An All-Atom Empiiical Eneigy Function
foi the Simulation of Nucleic Acius, BA GDA C-+DA H)6A, >>@, 11946-1197S (199S)

S. E. Fellei, B. Yin, R. W. Pastoi anu A. B. NacKeiell, }i., Noleculai Bynamics Simulation of
0nsatuiateu Lipius at Low Byuiation: Paiametiization anu Compaiison with Biffiaction Stuuies,
F.)4-0".6:I B)925:I, @=, 2269-2279 (1997) |alkenesj

R. B. Stote anu N. Kaiplus, Zinc Binuing in Pioteins anu Solution - A Simple but Accuiate Nonbonueu
Repiesentation, E2)*+.5", <=, 12-S1 (199S) |zinc ionj

Cuiient anu legacy paiametei values aie available fiom the CBARNN foice fielu web site on Alex
NacKeiell's Reseaich Inteiests page at the 0niveisity of Naiylanu School of Phaimacy,
https:ixsecuie.umaiylanu.euuieseaichamackeieieseaich.html

I(I&%2G'O
64 "#$%&' ()*+,) -./0* 64

Piotein-only paiameteis foi the eaily 199u's TINKER foice fielu with multipole values of Buuek anu
Ponuei. The cuiient file contains only the multipole values fiom the 199S papei by Buuek anu
Ponuei. This set is now supeiceeueu by the moie iecent TINKER foice fielu uevelopeu by Pengyu
Ren (see WATER.PRN, below).

N. }. Buuek anu }. W. Ponuei, Accuiate Electiostatic Nouelling of the Intiamoleculai Eneigy of
Pioteins, BA C)D49*A C-+DA, >B, 791-816 (199S)

&$?NI2G'O

ENCAB paiameteis foi pioteins anu nucleic acius. (&. 2*!2(*("&4.)

N. Levitt, N. Biishbeig, R. Shaion anu v. Baggett, Potential Eneigy Function anu Paiameteis foi
Simulations of the Noleculai Bynamics of Piotein anu Nucleic Acius in Solution, C)D4A E-0"A
C)DD95A, D>, 21S-2S1 (199S)

N. Levitt, N. Biishbeig, R. Shaion, K. E. Laiuig anu v. Baggett, Calibiation anu Testing of a Watei
Nouel foi Simulation of the Noleculai Bynamics of Piotein anu Nucleic Acius in Solution, BA E-0"A
C-+DA F, >?>, SuS1-Su61 (1997) |FSC wateij

YJ?Y2G'O

Simple NNR-N0E foice fielu of Boch anu Stein.

}. C. Boch anu A. S. Stein, A Nethou foi Beteimining 0veiall Piotein Folu fiom NNR Bistance
Restiaints, BA F.)D)IA (K@, <, SSS-S4S (1992)

OOD2G'O

Full NN2(1991) paiameteis incluuing #-systems. The anomeiic anu electionegativity coiiection
teims incluueu in some latei veisions of NN2 aie not implementeu.

N. L. Allingei, Confoimational Analysis. 1Su. NN2. A Byuiocaibon Foice Fielu 0tilizing v1 anu v2
Toisional Teims, BA GDA C-+DA H)6A, DD, 8127-81S4 (1977)

}. T. Spiague, }. C. Tai, Y. Yuh anu N. L. Allingei, The NNP2 Calculational Nethou, BA C)D49*A C-+DA, H,
S81-6uS (1987)

}. C. Tai anu N. L. Allingei, Noleculai Nechanics Calculations on Conjugateu Nitiogen-Containing
Beteiocycles, BA GDA C-+DA H)6A, >>?, 2uSu-2uSS (1988)

}. C. Tai, }.-B. Lii anu N. L. Allingei, A Noleculai Nechanics (NN2) Stuuy of Fuian, Thiophene, anu
Relateu Compounus, BA C)D49*A C-+DA, >?, 6SS-647 (1989)

N. L. Allingei, R. A. Kok anu N. R. Imam, Byuiogen Bonuing in NN2, BA C)D49*A C-+DA, D, S91-S9S
(1988)

L. Noiskov-Lauiitsen anu N. L. Allingei, A Noleculai Nechanics Tieatment of the Anomeiic Effect, BA
C)D49*A C-+DA, A, S26-SSS (1984)

All paiameteis uistiibuteu with TINKER aie fiom the ``NN2 (1991) Paiametei Set'', as pioviueu by
N. L. Allingei, 0niveisity of ueoigia
65 "#$%&' ()*+,) -./0* 65

OOL2G'O

Full NNS(2uuu) paiameteis incluuing pi-systems. The uiiectional hyuiogen bonuing teim anu
electionegativity bonu length coiiections aie implementeu, but the anomeiic anu Bohlmann
coiiection teims aie not implementeu.

N. L. Allingei, Y. B. Yuh anu }.-B. Lii, Noleculai Nechanics. The NNS Foice Fielu foi Byuiocaibons. 1,
BA GDA C-+DA H)6A, >>>, 8SS1-8S66 (1989)

}.-B. Lii anu N. L. Allingei, Noleculai Nechanics. The NNS Foice Fielu foi Byuiocaibons. 2.
vibiational Fiequencies anu Theimouynamics, BA GDA C-+DA H)6A, >>>, 8S66-8S7S (1989)

}.-B. Lii anu N. L. Allingei, Noleculai Nechanics. The NNS Foice Fielu foi Byuiocaibons. S. The van
uei Waals' Potentials anu Ciystal Bata foi Aliphatic anu Aiomatic Byuiocaibons, BA GDA C-+DA H)6A,
111, 8S76-8S82 (1989)

N. L. Allingei, B. }. ueise, W. Pyckhout, L. A. Paquette anu }. C. uallucci, Stiuctuies of Noiboinane anu
Bouecaheuiane by Noleculai Nechanics Calculations (NNS), X-iay Ciystallogiaphy, anu Election
Biffiaction, BA GDA C-+DA H)6A, >>>, 11u6-1114 (1989) |stietch-toision cioss teimj

N. L. Allingei, F. Li anu L. Yan, Noleculai Nechanics. The NNS Foice Fielu foi Alkenes, BA C)D49*A
C-+DA, >>, 848-867 (199u)

N. L. Allingei, F. Li, L. Yan anu }. C. Tai, Noleculai Nechanics (NNS) Calculations on Conjugateu
Byuiocaibons, BA C)D49*A C-+DA, >>, 868-89S (199u)

}.-B. Lii anu N. L. Allingei, Biiectional Byuiogen Bonuing in the NNS Foice Fielu. I, BA E-0"A L2MA
C-+DA, @, S91-6u9 (1994)

}.-B. Lii anu N. L. Allingei, Biiectional Byuiogen Bonuing in the NNS Foice Fielu. II, BA C)D49*A C-+DA,
>D, 1uu1-1u16 (1998)

All paiameteis uistiibuteu with TINKER aie fiom the ``NNS (2uuu) Paiametei Set'', as pioviueu by
N. L. Allingei, 0niveisity of ueoigia, August 2uuu

OOLG'J2G'O

Piotein-only veision of the NNS paiameteis.

}.-B. Lii anu N. L. Allingei, The NNS Foice Fielu foi Amiues, Polypeptiues anu Pioteins, BA C)D49*A
C-+DA, ><, 186-199 (1991)

JGP8(N2G'O

Complete 0PLS-0A with uniteu-atom paiameteis foi pioteins anu many classes of oiganic molecules.
Explicit hyuiogens on polai atoms anu aiomatic caibons.

W. L. }oigensen anu }. Tiiauo-Rives, The 0PLS Potential Functions foi Pioteins. Eneigy Ninimizations
foi Ciystals of Cyclic Peptiues anu Ciambin, BA GDA C-+DA H)6A, >>?, 16S7-1666 (1988) |peptiue anu
pioteinsj

66 "#$%&' ()*+,) -./0* 66
W. L. }oigensen anu B. L. Seveiance, Aiomatic-Aiomatic Inteiactions: Fiee Eneigy Piofiles foi the
Benzene Bimei in Watei, Chloiofoim, anu Liquiu Benzene, BA GDA C-+DA H)6A, >><, 4768-4774 (199u)
|aiomatic hyuiogensj

S. }. Weinei, P. A. Kollman, B. A. Case, 0. C. Singh, C. uhio, u. Alagona, S. Piofeta, }i. anu P. Weinei, A
New Foice Fielu foi Noleculai Nechanical Simulation of Nucleic Acius anu Pioteins, BA GDA C-+DA
H)6A, >?B, 76S-784 (1984) |uniteu-atom ``ANBER0PLS'' local geometiyj

S. }. Weinei, P. A. Kollman, B. T. Nguyen anu B. A. Case, An All Atom Foice Fielu foi Simulations of
Pioteins anu Nucleic Acius, BA C)D49*A C-+DA, @, 2Su-2S2 (1986) |all-atom "ANBER0PLS" local
geometiyj

L. X. Bang anu B. N. Pettitt, Simple Intiamoleculai Nouel Potentials foi Watei, BA E-0"A C-+DA, D>,
SS49-SSS4 (1987) |flexible TIPSP anu SPC wateij

W. L. }oigensen, }. B. Nauuia anu C. }. Swenson, 0ptimizeu Inteimoleculai Potential Functions foi
Liquiu Byuiocaibons, BA GDA C-+DA H)6A, >?B, 66S8-6646 (1984) |hyuiocaibonsj

W. L. }oigensen, E. R. Laiiu, T. B. Nguyen anu }. Tiiauo-Rives, Nonte Cailo Simulations of Puie Liquiu
Substituteu Benzenes with 0PLS Potential Functions, BA C)D49*A C-+DA, >E, 2u6-21S (199S)
|substituteu benzenesj

E. N. Buffy, P. }. Kowalczyk anu W. L. }oigensen, Bo Benatuiants Inteiact with Aiomatic
Byuiocaibons in Watei., BA GDA C-+DA H)6A, >>A, 9271-927S (199S) |benzene, naphthalene, uiea,
guaniuinium, tetiamethyl ammoniumj

W. L. }oigensen anu C. }. Swenson, 0ptimizeu Inteimoleculai Potential Functions foi Amiues anu
Peptiues. Stiuctuie anu Piopeities of Liquiu Amiues, BA GDA C-+DA H)6A, >?B, 76S-784 (1984)
|amiuesj

W. L. }oigensen, }. N. Biiggs anu N. L. Contieias, Relative Paitition Coefficients foi 0iganic Solutes
foim Fluiu Simulations, BA E-0"A C-+DA, DE, 168S-1686 (199u) |chloiofoim, pyiiuine, pyiazine,
pyiimiuinej

}. N. Biiggs, T. B. Nguyen anu W. L. }oigensen, Nonte Cailo Simulations of Liquiu Acetic Aciu anu
Nethyl Acetate with the 0PLS Potential Functions, BA E-0"A C-+DA, DA, SS1S-SS22 (1991) |acetic aciu,
methyl acetatej

B. Liu, F. Nullei-Plathe anu W. F. van uunsteien, A Foice Fielu foi Liquiu Bimethyl Sulfoxiue anu
Physical Piopeities of Liquiu Bimethyl Sulfoxiue Calculateu 0sing Noleculai Bynamics Simulation, BA
GDA C-+DA H)6A, >>@, 4S6S-4S66 (199S) |uimethyl sulfoxiuej

}. uao, X. Xia anu T. F. ueoige, Impoitance of Bimoleculai Inteiactions in Beveloping Empiiical
Potential Functions foi Liquiu Ammonia, BA E-0"A C-+DA, D@, 9241-9246 (199S) |ammoniaj

}. Aqvist, Ion-Watei Inteiaction Potentials Beiiveu fiom Fiee Eneigy Peituibation Simulations, BA
E-0"A C-+DA, DE, 8u21-8u24 (199u) |metal ionsj

W. S. Ross anu C. C. Baiuin, Ion-Inuuceu Stabilization of the u-BNA Quauiuplex: Fiee Eneigy
Peituibation Stuuies, BA GDA C-+DA H)6A, >>B, 4S6S-4S66 (1994) |alkali metal ionsj

}. Chanuiasekhai, B. C. Spellmeyei anu W. L. }oigensen, Eneigy Component Analysis foi Bilute
Aqueous Solutions of Li+, Na+, F-, anu Cl- Ions, BA GDA C-+DA H)6A, >?B, 9uS-91u (1984) |haliue ionsj
67 "#$%&' ()*+,) -./0* 67

Nost paiameteis uistiibuteu with TINKER aie fiom ``0PLS anu 0PLS-AA Paiameteis foi 0iganic
Nolecules, Ions, anu Nucleic Acius'' as pioviueu by W. L. }oigensen, Yale 0niveisity, 0ctobei 1997

JGP8NN2G'O

0PLS-AA foice fielu with all-atom paiameteis foi pioteins anu many geneial classes of oiganic
molecules.

W. L. }oigensen, B. S. Naxwell anu }. Tiiauo-Rives, Bevelopment anu Testing of the 0PLS All-Atom
Foice Fielu on Confoimational Eneigetics anu Piopeities of 0iganic Liquius, BA GDA C-+DA H)6A, >>@,
1122S-112S6 (1996)

B. S. Naxwell, }. Tiiauo-Rives anu W. L. }oigensen, A Compiehensive Stuuy of the Rotational Eneigy
Piofiles of 0iganic Systems by IF G.&"&4 N0 Theoiy, Foiming a Basis foi Peptiue Toisional
Paiameteis, BA C)D49*A C-+DA, >B, 984-1u1u (199S)

W. L. }oigensen anu N. A. NcBonalu, Bevelopment of an All-Atom Foice Fielu foi Beteiocycles.
Piopeities of Liquiu Pyiiuine anu Biazenes, <N?LCN?KOBA K)IA H*296*A, E<E, 14S-1SS (1998)

N. A. NcBonalu anu W. L. }oigensen, Bevelopment of an All-Atom Foice Fielu foi Beteiocycles.
Piopeities of Liquiu Pyiiole, Fuian, Biazoles, anu 0xazoles, BA E-0"A C-+DA F, >?<, 8u49-8uS9 (1998)

R. C. Rizzo anu W. L. }oigensen, 0PLS All-Atom Nouel foi Amines: Resolution of the Amine Byuiation
Pioblem, BA GDA C-+DA H)6A, ><>, 4827-48S6 (1999)

N. L. P. Piice, B. 0stiovsky anu W. L. }oigensen, uas-Phase anu Liquiu-State Piopeities of Esteis,
Nitiiles, anu Nitio Compounus with the 0PLS-AA Foice Fielu, BA C)D49*A C-+DA, <<, 1S4u-1SS2
(2uu1)

All paiameteis uistiibuteu with TINKER aie fiom ``0PLS anu 0PLS-AA Paiameteis foi 0iganic
Nolecules, Ions, anu Nucleic Acius'' as pioviueu by W. L. }oigensen, Yale 0niveisity, 0ctobei 1997

JGP8NNP2G'O

An impioveu 0PLS-AA paiametei set foi pioteins in which the only change is a iewoiking of many of
the backbone anu siuechain toisional paiameteis to give bettei agieement with LNP2 QN
calculations. This paiametei set is also known as 0PLS(2uuu).

u. A. Kaminsky, R. A. Fiiesnei, }. Tiiauo-Rives anu W. L. }oigensen, Evaluation anu Repaiametiization
of the 0PLS-AA Foice Fielu foi Pioteins via Compaiison with Accuiate Quantum Chemical
Calculations on Peptiues, BA E-0"A C-+DA F, >?A, 6474-6487 (2uu1)

8OJJ"Y2G'O

veision of 0PLS-0A foi use with potential smoothing. Laigely auapteu laigely fiom stanuaiu 0PLS-
0A paiameteis with mouifications to the vuw anu impiopei toision teims.

R. v. Pappu, R. K. Bait anu }. W. Ponuei, Analysis anu Application of Potential Eneigy Smoothing anu
Seaich Nethous foi ulobal 0ptimization, BA E-0"7 C-+DA F, >?<, 972S-9742 (1998) |smoothing
mouificationsj

8OJJ"YNN2G'O
68 "#$%&' ()*+,) -./0* 68

veision of 0PLS-AA foi use with potential smoothing. Laigely auapteu laigely fiom stanuaiu 0PLS-
AA paiameteis with mouifications to the vuw anu impiopei toision teims.

R. v. Pappu, R. K. Bait anu }. W. Ponuei, Analysis anu Application of Potential Eneigy Smoothing anu
Seaich Nethous foi ulobal 0ptimization, BA E-0"7 C-+DA F, >?<, 972S-9742 (1998) |smoothing
mouificationsj

<N"&'2G'O

The AN0EBA watei paiameteis foi a polaiizable atomic multipole electiostatics mouel. This mouel
is equal oi bettei to the best available watei mouels foi many bulk anu clustei piopeities.

P. Ren anu }. W. Ponuei, A Polaiizable Atomic Nultipole Watei Nouel foi Noleculai Nechanics
Simulation, BA E-0"A C-+DA F, >?@, S9SS-S947 (2uuS)

P. Ren anu }. W. Ponuei, Ion Solvation Theimouynamics fiom Simulation with a Polaiizable Foice
Fielu, A. uiossfielu, BA GDA C-+DA H)6A, ><A, 1S671-1S682 (2uuS)

P. Ren anu }. W. Ponuei, Tempeiatuie anu Piessuie Bepenuence of the AN0EBA Watei Nouel, BA
E-0"A C-+DA F, >?H, xxxx-xxxx (2uu4)

An eailiei veision the AN0EBA watei mouel is uesciibeu in: Yong Kong, Nultipole Electiostatic
Nethous foi Piotein Noueling with Reaction Fielu Tieatment, Biochemistiy & Noleculai Biophysics,
Washington 0niveisity, St. Louis, August, 1997 |available fiom http:uashei.wustl.euuponueij

69 "#$%&' ()*+,) -./0* 69
i2 I*)6+/@4/53) 59 "#$%&' '5.4/3*)
The uistiibution veision of the TINKER package contains ovei 7uu sepaiate piogiams, subioutines
anu functions. This section contains a biief uesciiption of the puipose of most of these coue units.
Fuithei infoimation can be founu in the comments locateu at the top of each souice coue file.

N?"#Z& 8.A+5.4/3*

"active" sets the list of atoms that aie useu uuiing each potential eneigy function calculation

NIIVN8& 8.A+5.4/3*

"auubase" builus the Caitesian cooiuinates foi a single nucleic aciu base; cooiuinates aie ieau fiom
the Piotein Bata Bank file oi founu fiom inteinal cooiuinates, then atom types aie assigneu anu
connectivity uata geneiateu

NIIVJ$I 8.A+5.4/3*

"auubonu" auus entiies to the attacheu atoms list in oiuei to geneiate a uiiect connection between
two atoms

NII8#I& 8.A+5.4/3*

"auusiue" builus the Caitesian cooiuinates foi a single amino aciu siue chain; cooiuinates aie ieau
fiom the Piotein Bata Bank file oi founu fiom inteinal cooiuinates, then atom types aie assigneu anu
connectivity uata geneiateu

NIeN?&$" >.364/53

"aujacent" finus an atom connecteu to atom "i1" othei than atom "i2"; if no such atom exists, then the
closest atom in space is ietuineu

NP?Y&OR G+5X+;C

"alchemy" computes the fiee eneigy uiffeience coiiesponuing to a small peituibation by Boltzmann
weighting the potential eneigy uiffeience ovei a numbei of sample states; cuiient veision
(incoiiectly) consiueis the chaige eneigy to be inteimoleculai in finuing the peituibation eneigies

N$NPR8#8 8.A+5.4/3*

"analysis" calls the seiies of ioutines neeueu to calculate the potential eneigy anu peifoim eneigy
paititioning analysis in teims of type of inteiaction oi atom numbei

N$NPRSW 8.A+5.4/3*

"analyz4" piints the eneigy to 4 uecimal places anu numbei of inteiactions foi each component of
the potential eneigy

N$NPRS] 8.A+5.4/3*
70 "#$%&' ()*+,) -./0* 70

"analyz6" piints the eneigy to 6 uecimal places anu numbei of inteiactions foi each component of
the potential eneigy

N$NPRSh 8.A+5.4/3*

"analyz8" piints the eneigy to 8 uecimal places anu numbei of inteiactions foi each component of
the potential eneigy

N$NPRS& G+5X+;C

"analyze" computes anu uisplays the total potential; options aie pioviueu to paitition the eneigy by
atom oi by potential function type; paiameteis useu in computing inteiactions can also be uisplayeu
by atom; output of laige eneigy inteiactions anu of electiostatic anu ineitial piopeities is available

N$-P&8 8.A+5.4/3*

"angles" finus the total numbei of bonu angles anu stoies the atom numbeis of the atoms uefining
each angle; foi each angle to a tiivalent cential atom, the thiiu bonueu atom is stoieu foi use in out-
of-plane benuing

N$$&NP G+5X+;C

"anneal" peifoims a simulateu annealing piotocol by means of vaiiable tempeiatuie moleculai
uynamics using eithei lineai, exponential oi sigmoiual cooling scheuules

N$J'O >.364/53

"anoim" finus the noim (length) of a vectoi; useu as a seivice ioutine by the Connolly suiface aiea
anu volume computation

N'?Y#Z& G+5X+;C

"aichive" is a utility piogiam foi cooiuinate files which concatenates multiple cooiuinate sets into a
single aichive file, oi extiacts inuiviuual cooiuinate sets fiom an aichive

N8&" 8.A+5.4/3*

"aset" computes by iecuision the A functions useu in the evaluation of Slatei-type (ST0) oveilap
integials

N"JORS& 8.A+5.4/3*

"atomyze" piints the potential eneigy components bioken uown by atom anu to a choice of piecision

N""N?Y 8.A+5.4/3*

"attach" geneiates lists of 1-S, 1-4 anu 1-S connectivities staiting fiom the pieviously ueteimineu list
of attacheu atoms (ie, 1-2 connectivity)

71 "#$%&' ()*+,) -./0* 71
VN8&>#P& 8.A+5.4/3*

"basefile" extiacts fiom an input filename the poition consisting of any uiiectoiy name anu the base
filename

V?(?J> 8.A+5.4/3*

"bcucof" ueteimines the coefficient matiix neeueu foi bicubic inteipolation of a function, giauients
anu cioss ueiivatives

V?(#$" 8.A+5.4/3*

"bcuint" peifoims a bicubic inteipolation of the function value on a 2B spline giiu

V?(#$"1 8.A+5.4/3*

"bcuint1" peifoims a bicubic inteipolation of the function value anu giauient along the uiiections of a
2B spline giiu

V?(#$"D 8.A+5.4/3*

"bcuint2" peifoims a bicubic inteipolation of the function value, giauient anu Bessain along the
uiiections of a 2B spline giiu

V&&ON$ 8.A+5.4/3*

"beeman" peifoims a single moleculai uynamics time step by means of a Beeman multistep iecuision
foimula; the actual coefficients aie Biooks' "Bettei Beeman" values

V&"N?> >.364/53

"betacf" computes a iapiuly conveigent continueu fiaction neeueu by ioutine "betai" to evaluate the
cumulative Beta uistiibution

V&"N# >.364/53

"betai" evaluates the cumulative Beta uistiibution function as the piobability that a ianuom vaiiable
fiom a uistiibution with Beta paiameteis "a" anu "b" will be less than "x"

V#-VPJ?% 8.A+5.4/3*

"bigblock" ieplicates the cooiuinates of a single unit cell to give a laigei block of iepeateu units

V#"J'8 8.A+5.4/3*

"bitois" finus the total numbei of bitoisions, paiis of oveilapping uiheuial angles, anu the numbeis of
the five atoms uefining each bitoision

VONQ >.364/53
72 "#$%&' ()*+,) -./0* 72

"bmax" computes the maximum oiuei of the B functions neeueu foi evaluation of Slatei-type (ST0)
oveilap integials

V$I&'' >.364/53

"bnueii" is the uistance bounu eiioi function anu ueiivatives; this veision implements the oiiginal
anu Bavel's noimalizeu lowei bounu penalty, the noimalizeu veision is piefeiieu when lowei
bounus aie small (as with NNR N0E iestiaints), the oiiginal penalty is neeueu if laige lowei bounus
aie piesent

VJ$I8 8.A+5.4/3*

"bonus" finus the total numbei of covalent bonus anu stoies the atom numbeis of the atoms uefining
each bonu

VJ'$ 8.A+5.4/3*

"boin" computes the Boin iauius of each atom foi use with the vaiious uBSA solvation mouels

VJ'$1 8.A+5.4/3*

"boin1" computes ueiivatives of the Boin iauii with iespect to atomic cooiuinates anu inciements
total eneigy ueiivatives anu viiial components foi potentials involving Boin iauii

VJ($I8 8.A+5.4/3*

"bounus" finus the centei of mass of each molecule anu tianslates any stiay molecules back into the
peiiouic box

V8&" 8.A+5.4/3*

"bset" computes by uownwaiu iecuision the B functions useu in the evaluation of Slatei-type (ST0)
oveilap integials

V8GP#$& 8.A+5.4/3*

"bspline" calculates the coefficients foi an n-th oiuei B-spline appioximation

V8GP#$&1 8.A+5.4/3*

"bspline1" calculates the coefficients anu ueiivative coefficients foi an n-th oiuei B-spline
appioximation

V88"&G 8.A+5.4/3*

"bsstep" takes a single Buliisch-Stoei step with monitoiing of local tiuncation eiioi to ensuie
accuiacy

?NP&$IN' 8.A+5.4/3*
73 "#$%&' ()*+,) -./0* 73

"calenuai" ietuins the cuiient time as a set of integei values iepiesenting the yeai, month, uay, houi,
minute anu seconu

?&PPN"JO 8.A+5.4/3*

"cellatom" completes the auuition of a symmetiy ielateu atom to a unit cell by upuating the atom
type anu attachment aiiays

?&$"&' 8.A+5.4/3*

"centei" moves the weighteu centioiu of each cooiuinate set to the oiigin uuiing least squaies
supeiposition

?&''J' 8.A+5.4/3*

"ceiioi" is the eiioi hanuling ioutine foi the Connolly suiface aiea anu volume computation

?>>"V 8.A+5.4/3*

"cfftb" computes the backwaiu complex uisciete Fouiiei tiansfoim, the Fouiiei synthesis

?>>"V1 8.A+5.4/3*

?>>"> 8.A+5.4/3*

"cfftf" computes the foiwaiu complex uisciete Fouiiei tiansfoim, the Fouiiei analysis

?>>">1 8.A+5.4/3*

?>>"# 8.A+5.4/3*

"cffti" initializes the aiiay "wsave" which is useu in both foiwaiu anu backwaiu tiansfoims; the
piime factoiization of "n" togethei with a tabulation of the tiigonometiic functions aie computeu anu
stoieu in "wsave"

?>>"#1 8.A+5.4/3*

?Y#'&' >.364/53

"chiiei" computes the chiiality eiioi anu its ueiivatives with iespect to atomic Caitesian cooiuinates
as a sum the squaies of ueviations of chiial volumes fiom taiget values

?Y%?PN8Y 8.A+5.4/3*

"chkclash" ueteimines if theie aie any atom clashes which might cause tiouble on subsequent eneigy
evaluation

?Y%GJP& 8.A+5.4/3*
74 "#$%&' ()*+,) -./0* 74

"chkpole" inveits atomic multipole moments as necessaiy at sites with chiial local iefeience fiame
uefinitions

?Y%'#$- 8.A+5.4/3*

"chkiing" tests angles to be constiaineu foi theii piesence in small iings anu iemoves constiaints
that aie ieuunuant

?Y%8#S& 8.A+5.4/3*

"chksize" computes a measuie of oveiall global stiuctuial expansion oi compaction fiom the numbei
of excess uppei oi lowei bounus matiix violations

?Y%"'&& 8.A+5.4/3*

"chktiee" tests a minimum eneigy stiuctuie to see if it belongs to the coiiect piogenitoi in the
existing map

?Y%QRS 8.A+5.4/3*

"chkxyz" finus any paiis of atoms with iuentical Caitesian cooiuinates, anu piints a waining message

?YJP&8%R 8.A+5.4/3*

"cholesky" uses a mouifieu Cholesky methou to solve the lineai system Ax = b, ietuining "x" in "b";
"A" is assumeu to be a ieal symmetiic positive uefinite matiix with its uiagonal anu uppei tiiangle
stoieu by iows

?#'GP$ 8.A+5.4/3*

?e%O >.364/53

"cjkm" computes the coefficients of spheiical haimonics expiesseu in piolate spheioiual cooiuinates

?P#OV&' 8.A+5.4/3*

?P#OV'-I 8.A+5.4/3*

?P#OV'J" 8.A+5.4/3*

?P#OV"J' 8.A+5.4/3*

?P#OVQRS 8.A+5.4/3*

?PJ?% 8.A+5.4/3*

"clock" ueteimines elapseu CP0 time in seconus since the stait of the job

75 "#$%&' ()*+,) -./0* 75
?P(8"&' 8.A+5.4/3*

"clustei" gets the paititioning of the system into gioups anu stoies a list of the gioup to which each
atom belongs

?JP(O$ 8.A+5.4/3*

"column" takes the off-uiagonal Bessian elements stoieu as spaise iows anu sets up inuices to allow
column access

?JOON$I 8.A+5.4/3*

"commanu" uses the stanuaiu 0nix-like iaigcgetaig ioutines to get the numbei anu values of
aiguments specifieu on the commanu line at piogiam iuntime

?JOG'&88 8.A+5.4/3*

"compiess" tiansfeis only the non-buiieu toii fiom the tempoiaiy toii aiiays to the final toii aiiays

?J$$&?" 8.A+5.4/3*

"connect" sets up the attacheu atom aiiays staiting fiom a set of inteinal cooiuinates

?J$$JPPR 8.A+5.4/3*

"connolly" uses the algoiithms fiom the ANSvAN piogiams of Nichael Connolly to compute the
analytical moleculai suiface aiea anu volume of a collection of spheiical atoms; thus it implements
Fieu Richaius' moleculai suiface uefinition as a set of analytically uefineu spheiical anu toioiual
polygons

?J$"N?" 8.A+5.4/3*

"contact" constiucts the contact suiface, cycles anu convex faces

?J$"'JP 8.A+5.4/3*

"contiol" gets initial values foi paiameteis that ueteimine the output style anu infoimation level
pioviueu by TINKER

?JJ'I8 8.A+5.4/3*

"cooius" conveits the thiee piincipal eigenvaluesvectois fiom the metiic matiix into atomic
cooiuinates, anu calls a ioutine to compute the ims ueviation fiom the bounus

?J''&PN"& G+5X+;C

"coiielate" computes the time coiielation function of some usei-supplieu piopeity fiom inuiviuual
snapshot fiames taken fiom a moleculai uynamics oi othei tiajectoiy

?'&N"&eZO 8.A+5.4/3*
76 "#$%&' ()*+,) -./0* 76

?'&N"&8&'Z&' 8.A+5.4/3*

?'&N"&8R8"&O 8.A+5.4/3*

?'&N"&(GIN"& 8.A+5.4/3*

?'R8"NP G+5X+;C

"ciystal" is a utility piogiam which conveits between fiactional anu Caitesian cooiuinates, anu can
geneiate full unit cells fiom asymmetiic units

?("J>>8 8.A+5.4/3*

"cutoffs" initializes anu stoies spheiical eneigy cutoff uistance winuows, Bessian element anu Ewalu
sum cutoffs, anu the paiiwise neighboi geneiation methou

?R"8R 8.A+5.4/3*

"cytsy" solves a system of lineai equations foi a cyclically tiiuiagonal, symmetiic, positive uefinite
matiix

?R"8RG 8.A+5.4/3*

"cytsyp" finus the Cholesky factois of a cyclically tiiuiagonal symmetiic, positive uefinite matiix
given by two vectois

?R"8R8 8.A+5.4/3*

"cytsys" solves a cyclically tiiuiagonal lineai system given the Cholesky factois

I1ID >.364/53

"u1u2" is a utility function useu in computation of the ieaction fielu iecuisive summation elements

I&P&"& 8.A+5.4/3*

"uelete" iemoves a specifieu atom fiom the Caitesian cooiuinates list anu shifts the iemaining atoms

I&G"Y >.364/53

I&8"'JReZO 8.A+5.4/3*

I&8"'JR8&'Z&' 8.A+5.4/3*

I>"OJI 8.A+5.4/3*

"uftmou" computes the mouulus of the uisciete Fouiiei tiansfoim of "bsaiiay", stoiing it into
"bsmou"
77 "#$%&' ()*+,) -./0* 77

I#N-K 8.A+5.4/3*

"uiagq" is a matiix uiagonalization ioutine which is ueiiveu fiom the classical given, housec, anu
eigen algoiithms with seveial mouifications to inciease the efficiency anu accuiacy

I#>>&K 8.A+5.4/3*

"uiffeq" peifoims the numeiical integiation of an oiuinaiy uiffeiential equation using an auaptive
stepsize methou to solve the coiiesponuing coupleu fiist-oiuei equations of the geneial foim uyiux
= f(x,y1,...,yn) foi yi = y1,...,yn

I#>>(8& G+5X+;C

"uiffuse" finus the self-uiffusion constant foi a homogeneous liquiu via the Einstein ielation fiom a
set of stoieu moleculai uynamics fiames; moleculai centeis of mass aie unfolueu anu mean squaieu
uisplacements aie computeu veisus time sepaiation

I#8"D >.364/53

"uist2" finus the uistance squaieu between two points; useu as a seivice ioutine by the Connolly
suiface aiea anu volume computation

I#8"-&JO G+5X+;C

"uistgeom" uses a metiic matiix uistance geometiy pioceuuie to geneiate stiuctuies with inteipoint
uistances that lie within specifieu bounus, with chiial centeis that maintain chiiality, anu with
toisional angles iestiaineu to uesiieu values; the usei also has the ability to inteiactively inspect anu
altei the tiiangle smootheu bounus matiix piioi to embeuuing

IOI(OG 8.A+5.4/3*

"umuump" puts the uistance matiix of the final stiuctuie into the uppei half of a matiix, the uistance
of each atom to the centioiu on the uiagonal, anu the inuiviuual teims of the bounus eiiois into the
lowei half of the matiix

IJ?(O&$" G+5X+;C

"uocument" geneiates a foimatteu uesciiption of all the coue mouules oi common blocks, an inuex of
ioutines calleu by each souice coue mouule, a listing of all valiu keywoius, a list of incluue file
uepenuencies as neeueu by a 0nix-style Nakefile, oi a foimatteu foice fielu paiametei set summaiy

IJ" >.364/53

"uot" finus the uot piouuct of two vectois

I8"ON" 8.A+5.4/3*

78 "#$%&' ()*+,) -./0* 78
"ustmat" selects a uistance matiix containing values between the pieviously smootheu uppei anu
lowei bounus; the uistance values aie chosen fiom unifoim uistiibutions, in a tiiangle coiielateu
fashion, oi using ianuom paitial metiization

IR$NO#? G+5X+;C

"uynamic" computes a moleculai uynamics tiajectoiy in any of seveial statistical mechanical
ensembles with optional peiiouic bounuaiies anu optional coupling to tempeiatuie anu piessuie
baths alteinatively a stochastic uynamics tiajectoiy can be geneiateu

&N$-N$- 8.A+5.4/3*

"eangang" calculates the angle-angle potential eneigy

&N$-N$-1 8.A+5.4/3*

"eangang1" calculates the angle-angle potential eneigy anu fiist ueiivatives with iespect to Caitesian
cooiuinates

&N$-N$-D 8.A+5.4/3*

"eangang2" calculates the angle-angle potential eneigy seconu ueiivatives with iespect to Caitesian
cooiuinates using finite uiffeience methous

&N$-N$-DN 8.A+5.4/3*

"eangang2a" calculates the angle-angle fiist ueiivatives foi a single inteiaction with iespect to
Caitesian cooiuinates; useu in computation of finite uiffeience seconu ueiivatives

&N$-N$-L 8.A+5.4/3*

"eangangS" calculates the angle-angle potential eneigy; also paititions the eneigy among the atoms

&N$-P& 8.A+5.4/3*

"eangle" calculates the angle benuing potential eneigy; piojecteu in-plane angles at tiigonal centeis
oi Fouiiei angle benuing teims aie optionally useu

&N$-P&1 8.A+5.4/3*

"eangle1" calculates the angle benuing potential eneigy anu the fiist ueiivatives with iespect to
Caitesian cooiuinates; piojecteu in-plane angles at tiigonal centeis oi Fouiiei angle benuing teims
aie optionally useu

&N$-P&D 8.A+5.4/3*

"eangle2" calculates seconu ueiivatives of the angle benuing eneigy foi a single atom using a mixtuie
of analytical anu finite uiffeience methous; piojecteu in-plane angles at tiigonal centeis oi Fouiiei
angle benuing teims aie optionally useu

79 "#$%&' ()*+,) -./0* 79
&N$-P&DN 8.A+5.4/3*

"eangle2a" calculates bonu angle benuing potential eneigy seconu ueiivatives with iespect to
Caitesian cooiuinates

&N$-P&DV 8.A+5.4/3*

"eangle2b" computes piojecteu in-plane benuing fiist ueiivatives foi a single angle with iespect to
Caitesian cooiuinates; useu in computation of finite uiffeience seconu ueiivatives

&N$-P&L 8.A+5.4/3*

"eangleS" calculates the angle benuing potential eneigy, also paititions the eneigy among the atoms;
piojecteu in-plane angles at tiigonal centeis oi Fouiiei angle benuing teims aie optionally useu

&VJ$I 8.A+5.4/3*

"ebonu" calculates the bonu stietching eneigy

&VJ$I1 8.A+5.4/3*

"ebonu1" calculates the bonu stietching eneigy anu fiist ueiivatives with iespect to Caitesian
cooiuinates

&VJ$ID 8.A+5.4/3*

"ebonu2" calculates seconu ueiivatives of the bonu stietching eneigy foi a single atom at a time

&VJ$IL 8.A+5.4/3*

"ebonuS" calculates the bonu stietching eneigy; also paititions the eneigy among the atoms

&V(?% 8.A+5.4/3*

"ebuck" calculates the Buckingham exp-6 van uei Waals eneigy

&V(?%TN 8.A+5.4/3*

"ebuckua" calculates the Buckingham exp-6 van uei Waals eneigy using a paiiwise uouble loop

&V(?%TV 8.A+5.4/3*

"ebuckub" calculates the Buckingham exp-6 van uei Waals eneigy using the methou of lights to
locate neighboiing atoms

&V(?%T? 8.A+5.4/3*

"ebuckuc" calculates the Buckingham exp-6 van uei Waals eneigy via a uaussian appioximation foi
potential eneigy smoothing
80 "#$%&' ()*+,) -./0* 80

&V(?%1 8.A+5.4/3*

"ebuck1" calculates the Buckingham exp-6 van uei Waals eneigy anu its fiist ueiivatives with iespect
to Caitesian cooiuinates

&V(?%1N 8.A+5.4/3*

"ebuck1a" calculates the Buckingham exp-6 van uei Waals eneigy anu its fiist ueiivatives using a
paiiwise uouble loop

&V(?%1V 8.A+5.4/3*

"ebuck1b" calculates the Buckingham exp-6 van uei Waals eneigy anu its fiist ueiivatives using the
methou of lights to locate neighboiing atoms

&V(?%1? 8.A+5.4/3*

"ebuck1c" calculates the Buckingham exp-6 van uei Waals eneigy anu its fiist ueiivatives via a
uaussian appioximation foi potential eneigy smoothing

&V(?%D 8.A+5.4/3*

"ebuck2" calculates the Buckingham exp-6 van uei Waals seconu ueiivatives foi a single atom at a
time

&V(?%DN 8.A+5.4/3*

"ebuck2a" calculates the Buckingham exp-6 van uei Waals seconu ueiivatives using a uouble loop
ovei ielevant atom paiis

&V(?%DV 8.A+5.4/3*

"ebuck2b" calculates the Buckingham exp-6 van uei Waals seconu ueiivatives via a uaussian
appioximation foi use with potential eneigy smoothing

&V(?%L 8.A+5.4/3*

"ebuckS" calculates the Buckingham exp-6 van uei Waals eneigy anu paititions the eneigy among
the atoms

&V(?%LN 8.A+5.4/3*

"ebuckSa" calculates the Buckingham exp-6 van uei Waals eneigy anu paititions the eneigy among
the atoms using a paiiwise uouble loop

&V(?%LV 8.A+5.4/3*

"ebuckSb" calculates the Buckingham exp-6 van uei Waals eneigy anu also paititions the eneigy
among the atoms using the methou of lights to locate neighboiing atoms
81 "#$%&' ()*+,) -./0* 81

&V(?%L? 8.A+5.4/3*

"ebuckSc" calculates the Buckingham exp-6 van uei Waals eneigy via a uaussian appioximation foi
potential eneigy smoothing

&?YN'-& 8.A+5.4/3*

"echaige" calculates the chaige-chaige inteiaction eneigy

&?YN'-&TN 8.A+5.4/3*

"echaigeua" calculates the chaige-chaige inteiaction eneigy using a paiiwise uouble loop

&?YN'-&TV 8.A+5.4/3*

"echaigeub" calculates the chaige-chaige inteiaction eneigy using the methou of lights to locate
neighboiing atoms

&?YN'-&T? 8.A+5.4/3*

"echaigeuc" calculates the chaige-chaige inteiaction eneigy foi use with potential smoothing
methous

&?YN'-&TI 8.A+5.4/3*

"echaigeuu" calculates the chaige-chaige inteiaction eneigy using a paiticle mesh Ewalu summation

&?YN'-&T& 8.A+5.4/3*

"echaigeue" calculates the chaige-chaige inteiaction eneigy using a paiticle mesh Ewalu summation
anu the methou of lights to locate neighboiing atoms

&?YN'-&1 8.A+5.4/3*

"echaige1" calculates the chaige-chaige inteiaction eneigy anu fiist ueiivatives with iespect to
Caitesian cooiuinates

&?YN'-&1N 8.A+5.4/3*

"echaige1a" calculates the chaige-chaige inteiaction eneigy anu fiist ueiivatives with iespect to
Caitesian cooiuinates using a paiiwise uouble loop

&?YN'-&1V 8.A+5.4/3*

"echaige1b" calculates the chaige-chaige inteiaction eneigy anu fiist ueiivatives with iespect to
Caitesian cooiuinates using the methou of lights to locate neighboiing atoms

&?YN'-&1? 8.A+5.4/3*
82 "#$%&' ()*+,) -./0* 82

"echaige1c" calculates the chaige-chaige inteiaction eneigy anu fiist ueiivatives with iespect to
Caitesian cooiuinates foi use with potential smoothing methous

&?YN'-&1I 8.A+5.4/3*

"echaige1u" calculates the chaige-chaige inteiaction eneigy anu fiist ueiivatives with iespect to
Caitesian cooiuinates using a paiticle mesh Ewalu summation

&?YN'-&D 8.A+5.4/3*

"echaige2" calculates seconu ueiivatives of the chaige-chaige inteiaction eneigy foi a single atom

&?YN'-&DN 8.A+5.4/3*

"echaige2a" calculates seconu ueiivatives of the chaige-chaige inteiaction eneigy foi a single atom
using a paiiwise uouble loop

&?YN'-&DV 8.A+5.4/3*

"echaige2b" calculates seconu ueiivatives of the chaige-chaige inteiaction eneigy foi a single atom
foi use with potential smoothing methous

&?YN'-&D? 8.A+5.4/3*

"echaige2c" calculates seconu ueiivatives of the chaige-chaige inteiaction eneigy foi a single atom
using a paiticle mesh Ewalu summation

&?YN'-&L 8.A+5.4/3*

"echaigeS" calculates the chaige-chaige inteiaction eneigy anu paititions the eneigy among the
atoms

&?YN'-&LN 8.A+5.4/3*

"echaigeSa" calculates the chaige-chaige inteiaction eneigy anu paititions the eneigy among the
atoms using a paiiwise uouble loop

&?YN'-&LV 8.A+5.4/3*

"echaigeSb" calculates the chaige-chaige inteiaction eneigy anu paititions the eneigy among the
atoms using the methou of lights to locate neighboiing atoms

&?YN'-&L? 8.A+5.4/3*

"echaigeSc" calculates the chaige-chaige inteiaction eneigy anu paititions the eneigy among the
atoms foi use with potential smoothing methous

&?YN'-&LI 8.A+5.4/3*
83 "#$%&' ()*+,) -./0* 83

"echaigeSu" calculates the chaige-chaige inteiaction eneigy anu paititions the eneigy among the
atoms using a paiticle mesh Ewalu summation

&?YN'-&L& 8.A+5.4/3*

"echaigeSe" calculates the chaige-chaige inteiaction eneigy anu paititions the eneigy among the
atoms using a paiticle mesh Ewalu summation anu the methou of lights to locate neighboiing atoms

&?Y-IGP 8.A+5.4/3*

"echgupl" calculates the chaige-uipole inteiaction eneigy

&?Y-IGP1 8.A+5.4/3*

"echgupl1" calculates the chaige-uipole inteiaction eneigy anu fiist ueiivatives with iespect to
Caitesian cooiuinates

&?Y-IGPD 8.A+5.4/3*

"echgupl2" calculates seconu ueiivatives of the chaige-uipole inteiaction eneigy foi a single atom

&?Y-IGPL 8.A+5.4/3*

"echguplS" calculates the chaige-uipole inteiaction eneigy; also paititions the eneigy among the
atoms

&I#GJP& 8.A+5.4/3*

"euipole" calculates the uipole-uipole inteiaction eneigy

&I#GJP&1 8.A+5.4/3*

"euipole1" calculates the uipole-uipole inteiaction eneigy anu fiist ueiivatives with iespect to
Caitesian cooiuinates

&I#GJP&D 8.A+5.4/3*

"euipole2" calculates seconu ueiivatives of the uipole-uipole inteiaction eneigy foi a single atom

&I#GJP&L 8.A+5.4/3*

"euipoleS" calculates the uipole-uipole inteiaction eneigy; also paititions the eneigy among the
atoms

&-N(88 8.A+5.4/3*

"egauss" calculates the uaussian expansion van uei Waals inteiaction eneigy

84 "#$%&' ()*+,) -./0* 84
&-N(88TN 8.A+5.4/3*

"egaussua" calculates the uaussian expansion van uei Waals inteiaction eneigy using a paiiwise
uouble loop

&-N(88TV 8.A+5.4/3*

"egaussub" calculates the uaussian expansion van uei Waals inteiaction eneigy foi use with potential
eneigy smoothing

&-N(881 8.A+5.4/3*

"egauss1" calculates the uaussian expansion van uei Waals inteiaction eneigy anu its fiist
ueiivatives with iespect to Caitesian cooiuinates

&-N(881N 8.A+5.4/3*

"egauss1a" calculates the uaussian expansion van uei Waals inteiaction eneigy anu its fiist
ueiivatives using a paiiwise uouble loop

&-N(881V 8.A+5.4/3*

"egauss1b" calculates the uaussian expansion van uei Waals inteiaction eneigy anu its fiist
ueiivatives foi use with stophat potential eneigy smoothing

&-N(88D 8.A+5.4/3*

"egauss2" calculates the uaussian expansion van uei Waals seconu ueiivatives foi a single atom at a
time

&-N(88DN 8.A+5.4/3*

"egauss2a" calculates the uaussian expansion van uei Waals seconu ueiivatives using a paiiwise
uouble loop

&-N(88DV 8.A+5.4/3*

"egauss2b" calculates the uaussian expansion van uei Waals seconu ueiivatives foi stophat potential
eneigy smoothing

&-N(88L 8.A+5.4/3*

"egaussS" calculates the uaussian expansion van uei Waals inteiaction eneigy anu paititions the
eneigy among the atoms

&-N(88LN 8.A+5.4/3*

"egaussSa" calculates the uaussian expansion van uei Waals inteiaction eneigy anu paititions the
eneigy among the atoms using a paiiwise uouble loop

85 "#$%&' ()*+,) -./0* 85
&-N(88LV 8.A+5.4/3*

"egaussSb" calculates the uaussian expansion van uei Waals inteiaction eneigy anu paititions the
eneigy among the atoms using a paiiwise uouble loop

&-V8NTN 8.A+5.4/3*

"egbsaua" calculates the geneializeu Boin polaiization eneigy foi the uBSA solvation mouels

&-V8NTV 8.A+5.4/3*

"egbsaub" calculates the geneializeu Boin polaiization eneigy foi the uBSA solvation mouels foi
use with potential smoothing methous via analogy to the smoothing of Coulomb's law

&-V8N1N 8.A+5.4/3*

"egbsa1a" calculates the geneializeu Boin eneigy anu fiist ueiivatives of the uBSA solvation mouels

&-V8N1V 8.A+5.4/3*

"egbsa1b" calculates the geneializeu Boin eneigy anu fiist ueiivatives of the uBSA solvation mouels
foi use with potential smoothing methous

&-V8NDN 8.A+5.4/3*

"egbsa2a" calculates seconu ueiivatives of the geneializeu Boin eneigy teim foi the uBSA solvation
mouels

&-V8NDV 8.A+5.4/3*

"egbsa2b" calculates seconu ueiivatives of the geneializeu Boin eneigy teim foi the uBSA solvation
mouels foi use with potential smoothing methous

&-V8NLN 8.A+5.4/3*

"egbsaSa" calculates the geneializeu Boin eneigy teim foi the uBSA solvation mouels; also
paititions the eneigy among the atoms

&-V8NLV 8.A+5.4/3*

"egbsaSb" calculates the geneializeu Boin polaiization eneigy foi the uBSA solvation mouels foi
use with potential smoothing methous via analogy to the smoothing of Coulomb's law; also paititions
the eneigy among the atoms

&-&JO 8.A+5.4/3*

"egeom" calculates the eneigy uue to iestiaints on positions, uistances, angles anu toisions as well as
uaussian basin anu spheiical uioplet iestiaints

&-&JO1 8.A+5.4/3*
86 "#$%&' ()*+,) -./0* 86

"egeom1" calculates the eneigy anu fiist ueiivatives with iespect to Caitesian cooiuinates uue to
iestiaints on positions, uistances, angles anu toisions as well as uaussian basin anu spheiical uioplet
iestiaints

&-&JOD 8.A+5.4/3*

"egeom2" calculates seconu ueiivatives of iestiaints on positions, uistances, angles anu toisions as
well as uaussian basin anu spheiical uioplet iestiaints

&-&JOL 8.A+5.4/3*

"egeomS" calculates the eneigy uue to iestiaints on positions, uistances, angles anu toisions as well
as uaussian basin anu uioplet iestiaints; also paititions eneigy among the atoms

&YNP 8.A+5.4/3*

"ehal" calculates the buffeieu 14-7 van uei Waals eneigy

&YNPTN 8.A+5.4/3*

"ehalua" calculates the buffeieu 14-7 van uei Waals eneigy using a paiiwise uouble loop

&YNPTV 8.A+5.4/3*

"ehalua" calculates the buffeieu 14-7 van uei Waals eneigy using the methou of lights to locate
neighboiing atoms

&YNP1 8.A+5.4/3*

"ehal1" calculates the buffeieu 14-7 van uei Waals eneigy anu its fiist ueiivatives with iespect to
Caitesian cooiuinates

&YNP1N 8.A+5.4/3*

"ehal1a" calculates the buffeieu 14-7 van uei Waals eneigy anu its fiist ueiivatives with iespect to
Caitesian cooiuinates using a paiiwise uouble loop

&YNP1V 8.A+5.4/3*

"ehal1b" calculates the buffeieu 14-7 van uei Waals eneigy anu its fiist ueiivatives with iespect to
Caitesian cooiuinates using the methou of lights to locate neighboiing atoms

&YNPD 8.A+5.4/3*

"ehal2" calculates the buffeieu 14-7 van uei Waals seconu ueiivatives foi a single atom at a time

&YNPL 8.A+5.4/3*

87 "#$%&' ()*+,) -./0* 87
"ehalS" calculates the buffeieu 14-7 van uei Waals eneigy anu paititions the eneigy among the
atoms

&YNPLN 8.A+5.4/3*

"ehalSa" calculates the buffeieu 14-7 van uei Waals eneigy anu paititions the eneigy among the
atoms using a paiiwise uouble loop

&YNPLV 8.A+5.4/3*

"ehalSb" calculates the buffeieu 14-7 van uei Waals eneigy anu also paititions the eneigy among the
atoms using the methou of lights to locate neighboiing atoms

&#-&$ 8.A+5.4/3*

"eigen" uses the powei methou to compute the laigest eigenvalues anu eigenvectois of the metiic
matiix, "valiu" is set tiue if the fiist thiee eigenvalues aie positive

&#-&$'-I 8.A+5.4/3*

&#-&$'J" 8.A+5.4/3*

&#-&$'J" 8.A+5.4/3*

&#-&$"J' 8.A+5.4/3*

&#-&$QRS 8.A+5.4/3*

&#OG'JG 8.A+5.4/3*

"eimpiop" calculates the impiopei uiheuial potential eneigy

&#OG'JG1 8.A+5.4/3*

"eimpiop1" calculates impiopei uiheuial eneigy anu its fiist ueiivatives with iespect to Caitesian
cooiuinates

&#OG'JGD 8.A+5.4/3*

"eimpiop2" calculates seconu ueiivatives of the impiopei uiheuial angle eneigy foi a single atom

&#OG'JGL 8.A+5.4/3*

"eimpiopS" calculates the impiopei uiheuial potential eneigy; also paititions the eneigy teims
among the atoms

&#OG"J' 8.A+5.4/3*

"eimptoi" calculates the impiopei toision potential eneigy
88 "#$%&' ()*+,) -./0* 88

&#OG"J'1 8.A+5.4/3*

"eimptoi1" calculates impiopei toision eneigy anu its fiist ueiivatives with iespect to Caitesian
cooiuinates

&#OG"J'D 8.A+5.4/3*

"eimptoi2" calculates seconu ueiivatives of the impiopei toision eneigy foi a single atom

&#OG"J'L 8.A+5.4/3*

"eimptoiS" calculates the impiopei toision potential eneigy; also paititions the eneigy teims among
the atoms

&Pe 8.A+5.4/3*

"elj" calculates the Lennaiu-}ones 6-12 van uei Waals eneigy

&PeTN 8.A+5.4/3*

"eljua" calculates the Lennaiu-}ones 6-12 van uei Waals eneigy using a paiiwise uouble loop

&PeTV 8.A+5.4/3*

"eljub" calculates the Lennaiu-}ones 6-12 van uei Waals eneigy using the methou of lights to locate
neighboiing atoms

&PeT? 8.A+5.4/3*

"eljuc" calculates the Lennaiu-}ones 6-12 van uei Waals eneigy via a uaussian appioximation foi
potential eneigy smoothing

&PeTI 8.A+5.4/3*

"eljuu" calculates the Lennaiu-}ones 6-12 van uei Waals eneigy foi use with stophat potential eneigy
smoothing

&Pe1 8.A+5.4/3*

"elj1" calculates the Lennaiu-}ones 6-12 van uei Waals eneigy anu its fiist ueiivatives with iespect to
Caitesian cooiuinates

&Pe1N 8.A+5.4/3*

"elj1a" calculates the Lennaiu-}ones 6-12 van uei Waals eneigy anu its fiist ueiivatives using a
paiiwise uouble loop

&Pe1V 8.A+5.4/3*
89 "#$%&' ()*+,) -./0* 89

"elj1b" calculates the Lennaiu-}ones 6-12 van uei Waals eneigy anu its fiist ueiivatives using the
methou of lights to locate neighboiing atoms

&Pe1? 8.A+5.4/3*

"elj1c" calculates the Lennaiu-}ones 6-12 van uei Waals eneigy anu its fiist ueiivatives via a
uaussian appioximation foi potential eneigy smoothing

&Pe1I 8.A+5.4/3*

"elj1u" calculates the van uei Waals inteiaction eneigy anu its fiist ueiivatives foi use with stophat
potential eneigy smoothing

&PeD 8.A+5.4/3*

"elj2" calculates the Lennaiu-}ones 6-12 van uei Waals seconu ueiivatives foi a single atom at a time

&PeDN 8.A+5.4/3*

"elj2a" calculates the Lennaiu-}ones 6-12 van uei Waals seconu ueiivatives using a uouble loop ovei
ielevant atom paiis

&PeDV 8.A+5.4/3*

"elj2b" calculates the Lennaiu-}ones 6-12 van uei Waals seconu ueiivatives via a uaussian
appioximation foi use with potential eneigy smoothing

&PeD? 8.A+5.4/3*

"elj2c" calculates the Lennaiu-}ones 6-12 van uei Waals seconu ueiivatives foi use with stophat
potential eneigy smoothing

&PeL 8.A+5.4/3*

"eljS" calculates the Lennaiu-}ones 6-12 van uei Waals eneigy anu also paititions the eneigy among
the atoms

&PeLN 8.A+5.4/3*

"eljSa" calculates the Lennaiu-}ones 6-12 van uei Waals eneigy anu also paititions the eneigy among
the atoms using a paiiwise uouble loop

&PeLV 8.A+5.4/3*

"eljSb" calculates the Lennaiu-}ones 6-12 van uei Waals eneigy anu also paititions the eneigy among
the atoms using the methou of lights to locate neighboiing atoms

&PeL? 8.A+5.4/3*
90 "#$%&' ()*+,) -./0* 90

"eljSc" calculates the Lennaiu-}ones 6-12 van uei Waals eneigy anu also paititions the eneigy among
the atoms via a uaussian appioximation foi potential eneigy smoothing

&PeLI 8.A+5.4/3*

"eljSu" calculates the Lennaiu-}ones 6-12 van uei Waals eneigy anu also paititions the eneigy among
the atoms foi use with stophat potential eneigy smoothing

&OV&I 8.A+5.4/3*

"embeu" is a uistance geometiy ioutine patteineu aftei the iueas of uoiuon Ciippen, Iiwin Kuntz anu
Tim Bavel; it takes as input a set of uppei anu lowei bounus on the inteipoint uistances, chiiality
iestiaints anu toisional iestiaints, anu attempts to geneiate a set of cooiuinates that satisfy the input
bounus anu iestiaints

&O&"NP 8.A+5.4/3*

"emetal" calculates the tiansition metal liganu fielu eneigy

&O&"NP1 8.A+5.4/3*

"emetal1" calculates the tiansition metal liganu fielu eneigy anu its fiist ueiivatives with iespect to
Caitesian cooiuinates

&O&"NPD 8.A+5.4/3*

"emetal2" calculates the tiansition metal liganu fielu seconu ueiivatives foi a single atom at a time

&O&"NPL 8.A+5.4/3*

"emetalS" calculates the tiansition metal liganu fielu eneigy anu also paititions the eneigy among the
atoms

&OOLYV 8.A+5.4/3*

"emmShb" calculates the NNS exp-6 van uei Waals anu uiiectional chaige tiansfei hyuiogen
bonuing eneigy

&OOLYVTN 8.A+5.4/3*

"emmShbua" calculates the NNS exp-6 van uei Waals anu uiiectional chaige tiansfei hyuiogen
bonuing eneigy using a paiiwise uouble loop

&OOLYVTV 8.A+5.4/3*

"emmShbub" calculates the NNS exp-6 van uei Waals anu uiiectional chaige tiansfei hyuiogen
bonuing eneigy using the methou of lights to locate neighboiing atoms

&OOLYV1 8.A+5.4/3*
91 "#$%&' ()*+,) -./0* 91

"emmShb1" calculates the NNS exp-6 van uei Waals anu uiiectional chaige tiansfei hyuiogen
bonuing eneigy with iespect to Caitesian cooiuinates

&OOLYV1N 8.A+5.4/3*

"emmShb1a" calculates the NNS exp-6 van uei Waals anu uiiectional chaige tiansfei hyuiogen
bonuing eneigy with iespect to Caitesian cooiuinates using a paiiwise uouble loop

&OOLYV1V 8.A+5.4/3*

"emmShb1b" calculates the NNS exp-6 van uei Waals anu uiiectional chaige tiansfei hyuiogen
bonuing eneigy with iespect to Caitesian cooiuinates using the methou of lights to locate
neighboiing atoms

&OOLYVD 8.A+5.4/3*

"emmShb2" calculates the NNS exp-6 van uei Waals anu uiiectional chaige tiansfei hyuiogen
bonuing seconu ueiivatives foi a single atom at a time

&OOLYVL 8.A+5.4/3*

"emmShbS" calculates the NNS exp-6 van uei Waals anu uiiectional chaige tiansfei hyuiogen
bonuing eneigy, anu paititions the eneigy among the atoms

&OOLYVLN 8.A+5.4/3*

"emmShbS" calculates the NNS exp-6 van uei Waals anu uiiectional chaige tiansfei hyuiogen
bonuing eneigy, anu paititions the eneigy among the atoms

&OOLYVLV 8.A+5.4/3*

"emmShbSb" calculates the NNS exp-6 van uei Waals anu uiiectional chaige tiansfei hyuiogen
bonuing eneigy using the methou of lights to locate neighboiing atoms

&OGJP& 8.A+5.4/3*

"empole" calculates the electiostatic eneigy uue to atomic multipole inteiactions anu uipole
polaiizability

&OGJP&TN 8.A+5.4/3*

"empoleua" calculates the electiostatic eneigy uue to atomic multipole inteiactions anu uipole
polaiizability using a paiiwise uouble loop

&OGJP&TV 8.A+5.4/3*

"empoleub" calculates the electiostatic eneigy uue to atomic multipole inteiactions anu uipole
polaiizability using a iegulai Ewalu summation

92 "#$%&' ()*+,) -./0* 92
&OGJP&1 8.A+5.4/3*

"empole1" calculates the multipole anu uipole polaiization eneigy anu ueiivatives with iespect to
Caitesian cooiuinates

&OGJP&1N 8.A+5.4/3*

"empole1a" calculates the multipole anu uipole polaiization eneigy anu ueiivatives with iespect to
Caitesian cooiuinates using a paiiwise uouble loop

&OGJP&1V 8.A+5.4/3*

"empole1b" calculates the multipole anu uipole polaiization eneigy anu ueiivatives with iespect to
Caitesian cooiuinates using a iegulai Ewalu summation

&OGJP&D 8.A+5.4/3*

"empole2" calculates seconu ueiivatives of the multipole anu uipole polaiization eneigy foi a single
atom at a time

&OGJP&DN 8.A+5.4/3*

"empole2a" computes multipole anu uipole polaiization fiist ueiivatives foi a single atom with
iespect to Caitesian cooiuinates; useu to get finite uiffeience seconu ueiivatives

&OGJP&L 8.A+5.4/3*

"empoleS" calculates the electiostatic eneigy uue to atomic multipole inteiactions anu uipole
polaiizability, anu paititions the eneigy among the atoms

&OGJP&LN 8.A+5.4/3*

"empoleSa" calculates the electiostatic eneigy uue to atomic multipole inteiactions anu uipole
polaiizability, anu paititions the eneigy among the atoms using a uouble loop

&OGJP&LV 8.A+5.4/3*

"empoleSb" calculates the electiostatic eneigy uue to atomic multipole inteiactions anu uipole
polaiizability, anu paititions the eneigy among the atoms using a iegulai Ewalu summation

&$&'-R >.364/53

"eneigy" calls the subioutines to calculate the potential eneigy teims anu sums up to foim the total
eneigy

&$'-RS& 8.A+5.4/3*

"eneigyze" is an auxiliaiy ioutine foi the analyze piogiam that peifoims the eneigy analysis anu
piints the total anu inteimoleculai eneigies

93 "#$%&' ()*+,) -./0* 93
&JGV&$I 8.A+5.4/3*

"eopbenu" computes the out-of-plane benu potential eneigy at tiigonal centeis via a Wilson-Becius-
Cioss angle benu

&JGV&$I1 8.A+5.4/3*

"eopbenu1" computes the out-of-plane benu potential eneigy anu fiist ueiivatives at tiigonal centeis
via a Wilson-Becius-Cioss angle benu

&JGV&$ID 8.A+5.4/3*

"eopbenu2" calculates seconu ueiivatives of the out-of-plane benu eneigy via a Wilson-Becius-Cioss
angle benu foi a single atom using finite uiffeience methous

&JGV&$IDN 8.A+5.4/3*

"eopbenu2a" calculates out-of-plane benuing fiist ueiivatives at a tiigonal centei via a Wilson-
Becius-Cioss angle benu; useu in computation of finite uiffeience seconu ueiivatives

&JGV&$IL 8.A+5.4/3*

"eopbenuS" computes the out-of-plane benu potential eneigy at tiigonal centeis via a Wilson-Becius-
Cioss angle benu; also paititions the eneigy among the atoms

&JGI#8" 8.A+5.4/3*

"eopuist" computes the out-of-plane uistance potential eneigy at tiigonal centeis via the cential
atom height

&JGI#8"1 8.A+5.4/3*

"eopuist1" computes the out-of-plane uistance potential eneigy anu fiist ueiivatives at tiigonal
centeis via the cential atom height

&JGI#8"D 8.A+5.4/3*

"eopuist2" calculates seconu ueiivatives of the out-of-plane uistance eneigy foi a single atom via the
cential atom height

&JGI#8"L 8.A+5.4/3*

"eopuistS" computes the out-of-plane uistance potential eneigy at tiigonal centeis via the cential
atom height; also paititions the eneigy among the atoms

&G#"J'8 8.A+5.4/3*

"epitois" calculates the pi-oibital toision potential eneigy

&G#"J'81 8.A+5.4/3*
94 "#$%&' ()*+,) -./0* 94

"epitois1" calculates the pi-oibital toision potential eneigy anu fiist ueiivatives with iespect to
Caitesian cooiuinates

&G#"J'8D 8.A+5.4/3*

"epitois2" calculates the seconu ueiivatives of the pi-oibital toision eneigy foi a single atom using
finite uiffeience methous

&G#"J'8DN 8.A+5.4/3*

"epitois2a" calculates the pi-oibital toision fiist ueiivatives; useu in computation of finite uiffeience
seconu ueiivatives

&G#"J'8L 8.A+5.4/3*

"epitoisS" calculates the pi-oibital toision potential eneigy; also paititions the eneigy teims among
the atoms

&GO& 8.A+5.4/3*

"epme" computes the iecipiocal space eneigy foi a paiticle mesh Ewalu summation ovei paitial
chaiges

&GO&1 8.A+5.4/3*

"epme1" computes the iecipiocal space eneigy anu fiist ueiivatives foi a paiticle mesh Ewalu
summation

&GO&L 8.A+5.4/3*

"epmeS" computes the iecipiocal space eneigy foi a paiticle mesh Ewalu summation ovei paitial
chaiges anu piints infoimation about the eneigy ovei the chaige giiu points

&G(?P? 8.A+5.4/3*

&'&NP 8.A+5.4/3*

"eieal" evaluates the ieal space poition of the iegulai Ewalu summation eneigy uue to atomic
multipole inteiactions anu uipole polaiizability

&'&NP1 8.A+5.4/3*

"eieal1" evaluates the ieal space poition of the iegulai Ewalu summation eneigy anu giauient uue to
atomic multipole inteiactions anu uipole polaiizability

&'&NPL 8.A+5.4/3*

"eiealS" evaluates the ieal space poition of the iegulai Ewalu summation eneigy uue to atomic
multipole inteiactions anu uipole polaiizability anu paititions the eneigy among the atoms
95 "#$%&' ()*+,) -./0* 95

&'&?#G 8.A+5.4/3*

"eiecip" evaluates the iecipiocal space poition of the iegulai Ewalu summation eneigy uue to atomic
multipole inteiactions anu uipole polaiizability

&'&?#G1 8.A+5.4/3*

"eiecip1" evaluates the iecipiocal space poition of the iegulai Ewalu summation eneigy anu
giauient uue to atomic multipole inteiactions anu uipole polaiizability

&'&?#GL 8.A+5.4/3*

"eiecipS" evaluates the iecipiocal space poition of the iegulai Ewalu summation eneigy uue to
atomic multipole inteiactions anu uipole polaiizability, anu piints infoimation about the eneigy ovei
the iecipiocal lattice vectois

&'> >.364/53

"eif" computes a numeiical appioximation to the value of the eiioi function via a Chebyshev
appioximation

&'>? >.364/53

"eifc" computes a numeiical appioximation to the value of the complementaiy eiioi function via a
Chebyshev appioximation

&'>?J'& 8.A+5.4/3*

"eifcoie" evaluates eif(x) oi eifc(x) foi a ieal aigument x; when calleu with moue set to u it ietuins
eif, a moue of 1 ietuins eifc; uses iational functions that appioximate eif(x) anu eifc(x) to at least 18
significant uecimal uigits

&'>#% 8.A+5.4/3*

"eifik" compute the ieaction fielu eneigy uue to a single paii of atomic multipoles

&'>#$Z >.364/53

"eifinv" evaluates the inveise of the eiioi function eif foi a ieal aigument in the iange (-1,1) using a
iational function appioximation followeu by cycles of Newton-Raphson coiiection

&'Q$>PI 8.A+5.4/3*

"eixnflu" calculates the macioscopic ieaction fielu eneigy aiising fiom a set of atomic multipoles

&'Q$>PI1 8.A+5.4/3*

"eixnflu1" calculates the macioscopic ieaction fielu eneigy anu ueiivatives with iespect to Caitesian
cooiuinates
96 "#$%&' ()*+,) -./0* 96

&'Q$>PID 8.A+5.4/3*

"eixnflu2" calculates seconu ueiivatives of the macioscopic ieaction fielu eneigy foi a single atom at
a time

&'Q$>PIL 8.A+5.4/3*

"eixnfluS" calculates the macioscopic ieaction fielu eneigy, anu also paititions the eneigy among the
atoms

&8JPZ 8.A+5.4/3*

"esolv" calculates the continuum solvation eneigy via eithei the Eisenbeig-NcLachlan ASP mouel,
0oi-Scheiaga SASA mouel, vaiious uBSA methous oi the ACE mouel

&8JPZ1 8.A+5.4/3*

"esolv1" calculates the continuum solvation eneigy anu fiist ueiivatives with iespect to Caitesian
cooiuinates using eithei the Eisenbeig-NcLachlan ASP, 0oi-Scheiaga SASA oi vaiious uBSA
solvation mouels

&8JPZD 8.A+5.4/3*

"esolv2" calculates seconu ueiivatives of the continuum solvation eneigy using eithei the Eisenbeig-
NcLachlan ASP, 0oi-Scheiaga SASA oi vaiious uBSA solvation mouels

&8JPZL 8.A+5.4/3*

"esolvS" calculates the continuum solvation eneigy using eithei the Eisenbeig-NcLachlan ASP mouel,
0oi-Scheiaga SASA mouel, vaiious uBSA methous oi the ACE mouel; also paititions the eneigy
among the atoms

&8"'V$I 8.A+5.4/3*

"estibnu" calculates the stietch-benu potential eneigy

&8"'V$I1 8.A+5.4/3*

"estibnu1" calculates the stietch-benu potential eneigy anu fiist ueiivatives with iespect to
Caitesian cooiuinates

&8"'V$ID 8.A+5.4/3*

"estibnu2" calculates the stietch-benu potential eneigy seconu ueiivatives with iespect to Caitesian
cooiuinates

&8"'V$IL 8.A+5.4/3*

"estibnuS" calculates the stietch-benu potential eneigy; also paititions the eneigy among the atoms
97 "#$%&' ()*+,) -./0* 97

&8"'"J' 8.A+5.4/3*

"estitoi" calculates the stietch-toision potential eneigy

&8"'"J'1 8.A+5.4/3*

"estitoi1" calculates the stietch-toision eneigy anu fiist ueiivatives with iespect to Caitesian
cooiuinates

&8"'"J'D 8.A+5.4/3*

"estitoi2" calculates the stietch-toision potential eneigy seconu ueiivatives with iespect to
Caitesian cooiuinates

&8"'"J'L 8.A+5.4/3*

"estitoiS" calculates the stietch-toision potential eneigy; also paititions the eneigy teims among the
atoms

&"J'8 8.A+5.4/3*

"etois" calculates the toisional potential eneigy

&"J'8TN 8.A+5.4/3*

"etoisua" calculates the toisional potential eneigy using a stanuaiu sum of Fouiiei teims

&"J'8TV 8.A+5.4/3*

"etoisub" calculates the toisional potential eneigy foi use with potential eneigy smoothing methous

&"J'81 8.A+5.4/3*

"etois1" calculates the toisional potential eneigy anu fiist ueiivatives with iespect to Caitesian
cooiuinates

&"J'81N 8.A+5.4/3*

"etois1a" calculates the toisional potential eneigy anu fiist ueiivatives with iespect to Caitesian
cooiuinates using a stanuaiu sum of Fouiiei teims

&"J'81V 8.A+5.4/3*

"etois1b" calculates the toisional potential eneigy anu fiist ueiivatives with iespect to Caitesian
cooiuinates foi use with potential eneigy smoothing methous

&"J'8D 8.A+5.4/3*

98 "#$%&' ()*+,) -./0* 98
"etois2" calculates the seconu ueiivatives of the toisional eneigy foi a single atom

&"J'8DN 8.A+5.4/3*

"etois2a" calculates the seconu ueiivatives of the toisional eneigy foi a single atom using a stanuaiu
sum of Fouiiei teims

&"J'8DV 8.A+5.4/3*

"etois2b" calculates the seconu ueiivatives of the toisional eneigy foi a single atom foi use with
potential eneigy smoothing methous

&"J'8L 8.A+5.4/3*

"etoisS" calculates the toisional potential eneigy; also paititions the eneigy among the atoms

&"J'8LN 8.A+5.4/3*

"etoisSa" calculates the toisional potential eneigy using a stanuaiu sum of Fouiiei teims anu
paititions the eneigy among the atoms

&"J'8LV 8.A+5.4/3*

"etoisSb" calculates the toisional potential eneigy foi use with potential eneigy smoothing methous
anu paititions the eneigy among the atoms

&"J'"J' 8.A+5.4/3*

"etoitoi" calculates the toision-toision potential eneigy

&"J'"J'1 8.A+5.4/3*

"etoitoi1" calculates the toision-toision eneigy anu fiist ueiivatives with iespect to Caitesian
cooiuinates

&"J'"J'D 8.A+5.4/3*

"etoitoi2" calculates the toision-toision potential eneigy seconu ueiivatives with iespect to
Caitesian cooiuinates

&"J'"J'L 8.A+5.4/3*

"etoitoiS" calculates the toision-toision potential eneigy; also paititions the eneigy teims among
the atoms

&('&R 8.A+5.4/3*

"euiey" calculates the 0iey-Biauley 1-S inteiaction eneigy

99 "#$%&' ()*+,) -./0* 99
&('&R1 8.A+5.4/3*

"euiey1" calculates the 0iey-Biauley inteiaction eneigy anu its fiist ueiivatives with iespect to
Caitesian cooiuinates

&('&RD 8.A+5.4/3*

"euiey2" calculates seconu ueiivatives of the 0iey-Biauley inteiaction eneigy foi a single atom at a
time

&('&RL 8.A+5.4/3*

"euieyS" calculates the 0iey-Biauley eneigy; also paititions the eneigy among the atoms

&<NPI?J> 8.A+5.4/3*

"ewalucof" finus a value of the Ewalu coefficient such that all teims beyonu the specifieu cutoff
uistance will have an value less than a specifieu toleiance

&QGPJ'& 8.A+5.4/3*

"exploie" uses simulateu annealing on an initial ciuue embeuueu uistance geoemtiy stiuctuie to
iefine veisus the bounu, chiiality, planaiity anu toisional eiioi functions

&Q"'N 8.A+5.4/3*

"extia" calculates any auuitional usei uefineu potential eneigy contiibution

&Q"'N1 8.A+5.4/3*

"extia1" calculates any auuitional usei uefineu potential eneigy contiibution anu its fiist ueiivatives

&Q"'ND 8.A+5.4/3*

"extia2" calculates seconu ueiivatives of any auuitional usei uefineu potential eneigy contiibution
foi a single atom at a time

&Q"'NL 8.A+5.4/3*

"extiaS" calculates any auuitional usei uefineu potential contiibution anu also paititions the eneigy
among the atoms

>N"NP 8.A+5.4/3*

"fatal" teiminates execution uue to a usei iequest, a seveie eiioi oi some othei nonstanuaiu
conuition

>>"VN?% 8.A+5.4/3*

100 "#$%&' ()*+,) -./0* 100
>>">'J$" 8.A+5.4/3*

>>"8&"(G 8.A+5.4/3*

>#&PI 8.A+5.4/3*

"fielu" sets the foice fielu potential eneigy functions fiom a paiametei file anu mouifications
specifieu in a keyfile

>#$NP 8.A+5.4/3*

"final" peifoims any final piogiam actions, piints a status message, anu then pauses if necessaiy to
avoiu closing the execution winuow

>#$IN"O 8.A+5.4/3*

"finuatm" locates a specific PBB atom name type within a iange of atoms fiom the PBB file, ietuins
zeio if the name type was not founu

>#QGIV 8.A+5.4/3*

"fixpub" coiiects pioblems with PBB files by conveiting iesiuue anu atom names to the foims useu
by TINKER

>'N?I#8" 8.A+5.4/3*

"fiacuist" computes a noimalizeu uistiibution of the paiiwise fiactional uistances between the
smootheu uppei anu lowei bounus

>'&&($#" >.364/53

"fieeunit" finus an unopeneu Foitian I0 unit anu ietuins its numeiical value fiom 1 to 99; the units
alieauy assigneu to "input" anu "iout" (usually S anu 6) aie skippeu since they have special meaning
as the uefault I0 units

-NOOP$ >.364/53

"gammln" uses a seiies expansion uue to Lanczos to compute the natuial logaiithm of the uamma
function at "x" in |u,1j

-IN G+5X+;C

"gua" implements uaussian Bensity Annealing (uBA) algoiithm foi global optimization via simulateu
annealing

-IN1 8.A+5.4/3*

-IND >.364/53

-INL 8.A+5.4/3*
101 "#$%&' ()*+,) -./0* 101

-IN8"N" 8.A+5.4/3*

-&$IJ" 8.A+5.4/3*

"genuot" finus the cooiuinates of a specifieu numbei of suiface points foi a spheie with the input
iauius anu cooiuinate centei

-&JI&8#? 8.A+5.4/3*

"geouesic" smooths the uppei anu lowei uistance bounus via the tiiangle inequality using a spaise
matiix veision of a shoitest path algoiithm

-&JO&"'R >.364/53

"geometiy" finus the value of the inteiatomic uistance, angle oi uiheuial angle uefineu by two to foui
input atoms

-&"VN8& 8.A+5.4/3*

"getbase" finus the base heavy atoms foi a single nucleotiue iesiuue anu copies the names anu
cooiuinates to the Piotein Bata Bank file

-&"#O& 8.A+5.4/3*

"getime" gets elapseu CP0 time in seconus foi an inteival

-&"#$" 8.A+5.4/3*

"getint" asks foi an inteinal cooiuinate file name, then ieaus the inteinal cooiuinates anu computes
Caitesian cooiuinates

-&"%&R 8.A+5.4/3*

"getkey" finus a valiu keyfile anu stoies its contents as line images foi subsequent keywoiu
paiametei seaiching

-&"OJPD 8.A+5.4/3*

"getmol2" asks foi a Sybyl N0L2 molecule file name, then ieaus the cooiuinates fiom the file

-&"OJ$#"J' 8.A+5.4/3*

-&"$(?Y 8.A+5.4/3*

"getnuch" finus the nucleotiue hyuiogen atoms foi a single iesiuue anu copies the names anu
cooiuinates to the Piotein Bata Bank file

-&"$(OV 8.A+5.4/3*
102 "#$%&' ()*+,) -./0* 102

"getnumb" seaichs an input stiing fiom left to iight foi an integei anu puts the numeiic value in
"numbei"; ietuins zeio with "next" unchangeu if no integei value is founu

-&"GIV 8.A+5.4/3*

"getpub" asks foi a Piotein Bata Bank file name, then ieaus in the cooiuinates file

-&"G'V 8.A+5.4/3*

"getpib" tests foi a possible piobe position at the inteiface between thiee neighboiing atoms

-&"G'O 8.A+5.4/3*

"getpim" finus the potential eneigy paiametei file anu then opens anu ieaus the paiameteis

-&"G'JY 8.A+5.4/3*

"getpioh" finus the hyuiogen atoms foi a single amino aciu iesiuue anu copies the names anu
cooiuinates to the Piotein Bata Bank file

-&"'&> 8.A+5.4/3*

"getief" copies stiuctuie infoimation fiom the iefeience aiea into the stanuaiu vaiiables foi the
cuiient system stiuctuie

-&"8&K 8.A+5.4/3*

"getseq" asks the usei foi the amino aciu sequence anu toisional angle values neeueu to uefine a
peptiue

-&"8&K$ 8.A+5.4/3*

"getseqn" asks the usei foi the nucleotiue sequence anu toisional angle values neeueu to uefine a
nucleic aciu

-&"8#I& 8.A+5.4/3*

"getsiue" finus the siue chain heavy atoms foi a single amino aciu iesiuue anu copies the names anu
cooiuinates to the Piotein Bata Bank file

-&"8"'#$- 8.A+5.4/3*

"getstiing" seaichs foi a quoteu text stiing within an input chaiactei stiing; the iegion between the
fiist anu seconu quotes is ietuineu as the "text"; if the actual text is too long, only the fiist pait is
ietuineu

-&""&Q" 8.A+5.4/3*

103 "#$%&' ()*+,) -./0* 103
"gettext" seaichs an input stiing foi the fiist stiing of non-blank chaiacteis; the iegion fiom a non-
blank chaiactei to the fiist blank space is ietuineu as "text"; if the actual text is too long, only the fiist
pait is ietuineu

-&""J' 8.A+5.4/3*

"gettoi" tests foi a possible toius position at the inteiface between two atoms, anu finus the toius
iauius, centei anu axis

-&"<J'I 8.A+5.4/3*

"getwoiu" seaichs an input stiing foi the fiist alphabetic chaiactei (A-Z oi a-z); the iegion fiom this
fiist chaiactei to the fiist blank space oi comma is ietuineu as a "woiu"; if the actual woiu is too
long, only the fiist pait is ietuineu

-&"QRS 8.A+5.4/3*

"getxyz" asks foi a Caitesian cooiuinate file name, then ieaus in the cooiuinates file

-'NI#&$" 8.A+5.4/3*

"giauient" calls subioutines to calculate the potential eneigy anu fiist ueiivatives with iespect to
Caitesian cooiuinates

-'NI'-I 8.A+5.4/3*

"giauigu" calls subioutines to calculate the potential eneigy anu fiist ueiivatives with iespect to
iigiu bouy cooiuinates

-'NI'J" 8.A+5.4/3*

"giauiot" calls subioutines to calculate the potential eneigy anu its toisional fiist ueiivatives

-'N>#? 8.A+5.4/3*

"giafic" outputs the uppei & lowei tiiangles anu uiagonal of a squaie matiix in a schematic foim foi
visual inspection

-'J(G8 8.A+5.4/3*

"gioups" tests a set of atoms to see if all aie membeis of a single atom gioup oi a paii of atom gioups;
if so, then the coiiect intia- oi inteigioup weight is assigneu

-'GP#$& 8.A+5.4/3*

"gipline" tests each atom gioup foi lineaiity of the sites containeu in the gioup

-R'N"& 8.A+5.4/3*

"gyiate" computes the iauius of gyiation of a moleculai system fiom its atomic cooiuinates
104 "#$%&' ()*+,) -./0* 104

YN$-P& 8.A+5.4/3*

"hangle" constiucts hybiiu angle benuing paiameteis given an initial state, final state anu "lambua"
value

YN"JO 8.A+5.4/3*

"hatom" assigns a new atom type to each hybiiu site

YVJ$I 8.A+5.4/3*

"hbonu" constiucts hybiiu bonu stietch paiameteis given an initial state, final state anu "lambua"
value

Y?YN'-& 8.A+5.4/3*

"hchaige" constiucts hybiiu chaige inteiaction paiameteis given an initial state, final state anu
"lambua" value

YI#GJP& 8.A+5.4/3*

"huipole" constiucts hybiiu uipole inteiaction paiameteis given an initial state, final state anu
"lambua" value

Y&88#N$ 8.A+5.4/3*

"hessian" calls subioutines to calculate the Bessian elements foi each atom in tuin with iespect to
Caitesian cooiuinates

Y&88'-I 8.A+5.4/3*

"hessigu" computes the numeiical Bessian elements with iespect to iigiu bouy cooiuinates via
6*ngioup+1 giauient evaluations

Y&88'J" 8.A+5.4/3*

"hessiot" computes the numeiical Bessian elements with iespect to toisional angles; eithei the full
matiix oi just the uiagonal can be calculateu; the full matiix neeus nomega+1 giauient evaluations
while the uiagonal iequiies just two giauient calls

Y#OG"J' 8.A+5.4/3*

"himptoi" constiucts hybiiu impiopei toisional paiameteis given an initial state, final state anu
"lambua" value

Y8"'V$I 8.A+5.4/3*

"hstibnu" constiucts hybiiu stietch-benu paiameteis given an initial state, final state anu "lambua"
value
105 "#$%&' ()*+,) -./0* 105

Y8"'"J' 8.A+5.4/3*

"hstitoi" constiucts hybiiu stietch-toision paiameteis given an initial state, final state anu "lambua"
value

Y"J'8 8.A+5.4/3*

"htois" constiucts hybiiu toisional paiameteis foi a given initial state, final state anu "lambua" value

YZI< 8.A+5.4/3*

"hvuw" constiucts hybiiu van uei Waals paiameteis given an initial state, final state anu "lambua"
value

YRV'#I 8.A+5.4/3*

"hybiiu" constiucts the hybiiu hamiltonian foi a specifieu initial state, final state anu mutation
paiametei "lambua"

#e%G"8 8.A+5.4/3*

"ijkpts" stoies a set of inuices useu uuiing calculation of macioscopic ieaction fielu eneigetics

#ON-& 8.A+5.4/3*

"image" takes the components of paiiwise uistance between two points in the same oi neighboiing
peiiouic boxes anu conveits to the components of the minimum image uistance

#OGJ8& 8.A+5.4/3*

"impose" peifoims the least squaies best supeiposition of two atomic cooiuinate sets via a
quateinion methou; upon ietuin, the fiist cooiuinate set is unchangeu while the seconu set is
tianslateu anu iotateu to give best fit; the final ioot mean squaie fit is ietuineu in "imsvalue"

#$I(?& 8.A+5.4/3*

"inuuce" computes the inuuceu uipole moment at each polaiizable site uue to uiiect oi mutual
polaiization; assumes that multipole components have alieauy been iotateu into the global
cooiuinate fiame

#$I(?&TN 8.A+5.4/3*

"inuuceua" computes the inuuceu uipole moment at each polaiizable site using a paiiwise uouble
loop

#$I(?&TV 8.A+5.4/3*

"inuuceub" computes the inuuceu uipole moment at each polaiizable site using a iegulai Ewalu
summation
106 "#$%&' ()*+,) -./0* 106

#$&I-& 8.A+5.4/3*

"ineuge" inseits a concave euge into the linkeu list foi its tempoiaiy toius

#$&'"#N 8.A+5.4/3*

"ineitia" computes the piincipal moments of ineitia foi the system, anu optionally tianslates the
centei of mass to the oiigin anu iotates the piincipal axes onto the global axes

#$#"&'' >.364/53

"initeii" is the initial eiioi function anu ueiivatives foi a uistance geometiy embeuuing; it incluues
components fiom the local geometiy anu toisional iestiaint eiiois

#$#"#NP 8.A+5.4/3*

"initial" sets up oiiginal values foi some paiameteis anu vaiiables that might not otheiwise get
initializeu

#$#"G'O 8.A+5.4/3*

"initpim" completely initializes a foice fielu by setting all paiameteis to zeio anu using uefaults foi
contiol values

#$#"'&8 8.A+5.4/3*

"inities" sets names foi biopolymei iesiuue types useu in PBB file conveision anu automateu
geneiation of stiuctuies

#$#"'J" 8.A+5.4/3*

"initiot" sets the toisional angles which aie to be iotateu in subsequent computation, by uefault
automatically selects all iotatable single bonus; assumes inteinal cooiuinates have alieauy been
setup

#$8&'" 8.A+5.4/3*

"inseit" auus the specifieu atom to the Caitesian cooiuinates list anu shifts the iemaining atoms

#$"&I#" G+5X+;C

"inteuit" allows the usei to extiact infoimation fiom oi altei the values within an inteinal
cooiuinates file

#$"QRS G+5X+;C

"intxyz" takes as input an inteinal cooiuinates file, conveits to anu then wiites out Caitesian
cooiuinates
107 "#$%&' ()*+,) -./0* 107

#$ZV&"N >.364/53

"invbeta" computes the inveise Beta uistiibution function via a combination of Newton iteiation anu
bisection seaich

#$Z&'" 8.A+5.4/3*

"inveit" inveits a matiix using the uauss-}oiuan methou

#G&I-& 8.A+5.4/3*

"ipeuge" inseits convex euge into linkeu list foi atom

#8GPG& 8.A+5.4/3*

"isplpe" computes the coefficients foi a cubic peiiouic inteipolating spline

eN?JV# 8.A+5.4/3*

"jacobi" peifoims a matiix uiagonalization of a ieal symmetiic matiix by the methou of }acobi
iotations

%N$-N$- 8.A+5.4/3*

"kangang" assigns the paiameteis foi angle-angle cioss teim inteiactions anu piocesses new oi
changeu paiametei values

%N$-P& 8.A+5.4/3*

"kangle" assigns the foice constants anu iueal angles foi the bonu angles; also piocesses new oi
changeu paiameteis

%N"JO 8.A+5.4/3*

"katom" assigns an atom type uefinitions to each atom in the stiuctuie anu piocesses any new oi
changeu values

%VJ$I 8.A+5.4/3*

"kbonu" assigns a foice constant anu iueal bonu length to each bonu in the stiuctuie anu piocesses
any new oi changeu paiametei values

%?YN'-& 8.A+5.4/3*

"kchaige" assigns paitial chaiges to the atoms within the stiuctuie anu piocesses any new oi
changeu values

%?Y#'NP 8.A+5.4/3*
108 "#$%&' ()*+,) -./0* 108

"kchiial" ueteimines the taiget value foi each chiiality anu planaiity iestiaint as the signeu volume
of the paiallelpipeu spanneu by vectois fiom a common atom to each of thiee othei atoms

%I#GJP& 8.A+5.4/3*

"kuipole" assigns bonu uipoles to the bonus within the stiuctuie anu piocesses any new oi changeu
values

%&$&- 8.A+5.4/3*

"keneg" applies piimaiy anu seconuaiy electionegativity bonu length coiiections to applicable bonu
paiameteis

%&<NPI 8.A+5.4/3*

"kewalu" assigns both iegulai Ewalu summation anu paiticle mesh Ewalu paiameteis foi a peiiouic
box

%-&JO 8.A+5.4/3*

"kgeom" asisgns paiameteis foi geometiic iestiaint teims to be incluueu in the potential eneigy
calculation

%#OG'JG 8.A+5.4/3*

"kimpiop" assigns potential paiameteis to each impiopei uiheuial in the stiuctuie anu piocesses
any changeu values

%#OG"J' 8.A+5.4/3*

"kimptoi" assigns toisional paiameteis to each impiopei toision in the stiuctuie anu piocesses any
changeu values

%#$&"#? 8.A+5.4/3*

"kinetic" computes the total kinetic eneigy anu kinetic eneigy contiibutions to the piessuie tensoi
by summing ovei velocities

%O&"NP 8.A+5.4/3*

"kmetal" assigns liganu fielu paiameteis to tiansition metal atoms anu piocesses any new oi
changeu paiametei values

%OGJP& 8.A+5.4/3*

"kmpole" assigns atomic multipole moments to the atoms of the stiuctuie anu piocesses any new oi
changeu values

%JGV&$I 8.A+5.4/3*
109 "#$%&' ()*+,) -./0* 109

"kopbenu" assigns the foice constants foi out-of-plane benuing at tiigonal centeis via Wilson-Becius-
Cioss angle benus; also piocesses any new oi changeu paiametei values

%JGI#8" 8.A+5.4/3*

"kopuist" assigns the foice constants foi out-of-plane uistance at tiigonal centeis via the cential atom
height; also piocesses any new oi changeu paiametei values

%J'V#" 8.A+5.4/3*

"koibit" assigns pi-oibital paiameteis to conjugateu systems anu piocesses any new oi changeu
paiameteis

%G#"J'8 8.A+5.4/3*

"kpitois" assigns pi-oibital toision paiameteis to toisions neeuing them, anu piocesses any new oi
changeu values

%GJPN' 8.A+5.4/3*

"kpolai" assigns atomic uipole polaiizabilities to the atoms within the stiuctuie anu piocesses any
new oi changeu values

%8JPZ 8.A+5.4/3*

"ksolv" assigns continuum solvation eneigy paiameteis foi the Eisenbeig-NcLachlan ASP, 0oi-
Scheiaga SASA oi vaiious uBSA solvation mouels

%8"'V$I 8.A+5.4/3*

"kstibnu" assigns the paiameteis foi the stietch-benu inteiactions anu piocesses new oi changeu
paiametei values

%8"'"J' 8.A+5.4/3*

"kstitoi" assigns stietch-toision paiameteis to toisions neeuing them, anu piocesses any new oi
changeu values

%"J'8 8.A+5.4/3*

"ktois" assigns toisional paiameteis to each toision in the stiuctuie anu piocesses any new oi
changeu values

%"J'"J' 8.A+5.4/3*

"ktoitoi" assigns toision-toision paiameteis to aujacent toision paiis anu piocesses any new oi
changeu values

%('&R 8.A+5.4/3*
110 "#$%&' ()*+,) -./0* 110

"kuiey" assigns the foice constants anu iueal uistances foi the 0iey-Biauley 1-S inteiactions; also
piocesses any new oi changeu paiametei values

%ZI< 8.A+5.4/3*

"kvuw" assigns the paiameteis to be useu in computing the van uei Waals inteiactions anu piocesses
any new oi changeu values foi these paiameteis

PN""#?& 8.A+5.4/3*

"lattice" stoies the peiiouic box uimensions anu sets angle values to be useu in computing fiactional
cooiuinates

PV>-8 8.A+5.4/3*

"lbfgs" is a limiteu memoiy BFuS quasi-newton nonlineai optimization ioutine

P#-N8& 8.A+5.4/3*

"ligase" tianslates a nucleic aciu stiuctuie in Piotein Bata Bank foimat to a Caitesian cooiuinate file
anu sequence file

P#-Y"8 8.A+5.4/3*

"lights" computes the set of neaiest neighboi inteiactions using the methou of lights algoiithm

P#$VJIR 8.A+5.4/3*

"linbouy" finus the angulai velocity of a lineai iigiu bouy given the ineitia tensoi anu angulai
momentum

PO8"&G 8.A+5.4/3*

"lmstep" computes the Levenbeig-Naiquaiut step uuiing a nonlineai least squaies calculation; this
veision is baseu upon iueas fiom the Ninpack ioutine LNPAR togethei with with the inteinal
uoubling stiategy of Bennis anu Schnabel

PJ?NPO#$ 8.A+5.4/3*

"localmin" is useu uuiing noimal moue local seaich to peifoim a Caitesian cooiuinate eneigy
minimization

PJ?NP'-I 8.A+5.4/3*

"localigu" is useu uuiing the PSS local seaich pioceuuie to peifoim a iigiu bouy eneigy minimization

PJ?NP'J" 8.A+5.4/3*

111 "#$%&' ()*+,) -./0* 111
"localiot" is useu uuiing the PSS local seaich pioceuuie to peifoim a toisional space eneigy
minimization

PJ?NPQRS 8.A+5.4/3*

"localxyz" is useu uuiing the potential smoothing anu seaich pioceuuie to peifoim a local
optimization at the cuiient smoothing level

PJ?&'' >.364/53

"loceii" is the local geometiy eiioi function anu ueiivatives incluuing the 1-2, 1-S anu 1-4 uistance
bounu iestiaints

PJ<?N8& 8.A+5.4/3*

"lowcase" conveits a text stiing to all lowei case letteis

ONeJ'#S& 8.A+5.4/3*

"majoiize" iefines the piojecteu cooiuinates by attempting to minimize the least squaie iesiuual
between the tiial uistance matiix anu the uistances computeu fiom the cooiuinates

ON%&#$" 8.A+5.4/3*

"makeint" conveits Caitesian to inteinal cooiuinates wheie selection of inteinal cooiuinates is
contiolleu by "moue"

ON%&GIV 8.A+5.4/3*

"makexyz" conveits a set of Caitesian cooiuinates to Piotein Bata Bank foimat with special hanuling
foi systems consisting of polypeptiue chains, liganus anu watei molecules

ON%&'&> 8.A+5.4/3*

"makeief" copies the infoimation containeu in the "xyz" file of the cuiient stiuctuie into
coiiesponuing iefeience aieas

ON%&QRS 8.A+5.4/3*

"makexyz" geneiates a complete set of Caitesian cooiuinates foi a full stiuctuie fiom the inteinal
cooiuinate values

ONG?Y&?% 8.A+5.4/3*

"mapcheck" checks the cuiient minimum eneigy stiuctuie foi possible auuition to the mastei list of
local minima

ONQ<&PP >.364/53

112 "#$%&' ()*+,) -./0* 112
"maxwell" ietuins a speeu in Angstiomspicoseconu ianuomly selecteu fiom a S-B Naxwell-
Boltzmann uistiibution foi the specifieu paiticle mass anu system tempeiatuie

O?O1 >.364/53

"mcm1" is a seivice ioutine that computes the eneigy anu giauient foi tiuncateu Newton
optimization in Caitesian cooiuinate space

O?OD 8.A+5.4/3*

"mcm2" is a seivice ioutine that computes the spaise matiix Bessian elements foi tiuncateu Newton
optimization in Caitesian cooiuinate space

O?O8"&G >.364/53

"mcmstep" implements the minimization phase of an NCN step via Caitesian minimization following
a Nonte Cailo step

OI#$#" 8.A+5.4/3*

"muinit" initializes the velocities anu acceleiations foi a moleculai uynamics tiajectoiy, incluuing
iestaits

OI'&8" 8.A+5.4/3*

"muiest" finus anu iemoves any tianslational oi iotational kinetic eneigy of the oveiall system
centei of mass

OI8NZ& 8.A+5.4/3*

"musave" wiites moleculai uynamics tiajectoiy snapshots anu auxiliaiy files with velocity anu
inuuceu uipole infoimation; also checks foi usei iequesteu teimination of a simulation

OI8"N" 8.A+5.4/3*

"mustat" is calleu at each moleculai uynamics time step to foim statistics on vaiious aveiage values
anu fluctuations, anu to peiiouically save the state of the tiajectoiy

O&N8>$ 8.A+5.4/3*

O&N8>G 8.A+5.4/3*

O&N8>8 8.A+5.4/3*

O&N8GO 8.A+5.4/3*

"measpm" computes the volume of a single piism section of the full inteiioi polyheuion

O&?YN$#? 8.A+5.4/3*
113 "#$%&' ()*+,) -./0* 113

"mechanic" sets up neeueu paiameteis foi the potential eneigy calculation anu ieaus in many of the
usei selectable options

O&'-& 8.A+5.4/3*

"meige" combines the iefeience anu cuiient stiuctuies into a single new "cuiient" stiuctuie
containing the iefeience atoms followeu by the atoms of the cuiient stiuctuie

O&"'#? 8.A+5.4/3*

"metiic" takes as input the tiial uistance matiix anu computes the metiic matiix of all possible uot
piouucts between the atomic vectois anu the centei of mass using the law of cosines anu the
following foimula foi the uistances to the centei of mass:

O#I&'' >.364/53

"miueii" is the seconuaiy eiioi function anu ueiivatives foi a uistance geometiy embeuuing; it
incluues components fiom the uistance bounus, local geometiy, chiiality anu toisional iestiaint
eiiois

O#$#O#S1 >.364/53

"minimiz1" is a seivice ioutine that computes the eneigy anu giauient foi a low stoiage BFuS
optimization in Caitesian cooiuinate space

O#$#O#S& G+5X+;C

"minimize" peifoims eneigy minimization in Caitesian cooiuinate space using a low stoiage BFuS
nonlineai optimization

O#$#'J" G+5X+;C

"miniiot" peifoims an eneigy minimization in toisional angle space using a low stoiage BFuS
nonlineai optimization

O#$#'J"1 >.364/53

"miniiot1" is a seivice ioutine that computes the eneigy anu giauient foi a low stoiage BFuS
nonlineai optimization in toisional angle space

O#$GN"Y 8.A+5.4/3*

"minpath" is a ioutine foi finuing the tiiangle smootheu uppei anu lowei bounus of each atom to a
specifieu ioot atom using a spaise vaiiant of the Bellman-Foiu shoitest path algoiithm

O#$'#-#I G+5X+;C

"miniigiu" peifoims an eneigy minimization of iigiu bouy atom gioups using a low stoiage BFuS
nonlineai optimization
114 "#$%&' ()*+,) -./0* 114

O#$'#-#I1 >.364/53

"miniigiu1" is a seivice ioutine that computes the eneigy anu giauient foi a low stoiage BFuS
nonlineai optimization of iigiu bouies

OO#I 8.A+5.4/3*

"mmiu" implements a mouifieu miupoint methou to auvance the integiation of a set of fiist oiuei
uiffeiential equations

OJI&?N'" 8.A+5.4/3*

OJI&'J" 8.A+5.4/3*

OJI&8'?Y 8.A+5.4/3*

OJI&"J'8 8.A+5.4/3*

OJI(P# 8.A+5.4/3*

"mouuli" sets the mouuli of the inveise uisciete Fouiiei tiansfoim of the B-splines; bsmou|1-Sj holu
these values, nfft|1-Sj aie the giiu uimensions, bsoiuei is the oiuei of B-spline appioximation

OJP&?(P& 8.A+5.4/3*

"molecule" counts the molecules, assigns each atom to its molecule anu computes the mass of each
molecule

OJP(#$I 8.A+5.4/3*

"moluinu" computes the moleculai inuuceu uipole components in the piesence of an exteinal electiic
fielu

OJO&$"8 8.A+5.4/3*

"moments" computes the total electiic chaige, uipole anu quauiupole moments foi the entiie system
as a sum ovei the paitial chaiges, bonu uipoles anu atomic multipole moments

OJ$"& G+5X+;C

"monte" peifoims a Nonte CailoNCN confoimational seaich using eithei Caitesian single atom oi
toisional move sets

O("N"& 8.A+5.4/3*

"mutate" constiucts the hybiiu hamiltonian foi a specifieu initial state, final state anu mutation
paiametei "lambua"

115 "#$%&' ()*+,) -./0* 115
$&&I(GIN"& 8.A+5.4/3*

$&#-YVJ' 8.A+5.4/3*

"neighboi" finus all of the neighbois of each atom

$&<N"O 8.A+5.4/3*

"newatm" cieates anu uefines an atom neeueu foi the Caitesian cooiuinates file, but which may not
piesent in the oiiginal Piotein Bata Bank file

$&<"J$ G+5X+;C

"newton" peifoims an eneigy minimization in Caitesian cooiuinate space using a tiuncateu Newton
methou

$&<"J$1 >.364/53

"newton1" is a seivice ioutine that computes the eneigy anu giauient foi tiuncateu Newton
optimization in Caitesian cooiuinate space

$&<"J$D 8.A+5.4/3*

"newton2" is a seivice ioutine that computes the spaise matiix Bessian elements foi tiuncateu
Newton optimization in Caitesian cooiuinate space

$&<"'J" G+5X+;C

"newtiot" peifoims an eneigy minimization in toisional angle space using a tiuncateu Newton
conjugate giauient methou

$&<"'J"1 >.364/53

"newtiot1" is a seivice ioutine that computes the eneigy anu giauient foi tiuncateu Newton
conjugate giauient optimization in toisional angle space

$&<"'J"D 8.A+5.4/3*

"newtiot2" is a seivice ioutine that computes the spaise matiix Bessian elements foi tiuncateu
Newton optimization in toisional angle space

$&Q"N'- 8.A+5.4/3*

"nextaig" finus the next unuseu commanu line aigument anu ietuins it in the input chaiactei stiing

$&Q""&Q" >.364/53

"nexttext" finus anu ietuins the location of the fiist non-blank chaiactei within an input text stiing;
zeio is ietuineu if no such chaiactei is founu
116 "#$%&' ()*+,) -./0* 116

$J'ONP >.364/53

"noimal" geneiates a ianuom numbei fiom a noimal uaussian uistiibution with a mean of zeio anu a
vaiiance of one

$(?VN8& 8.A+5.4/3*

"nucbase" builus the siue chain foi a single nucleotiue base in teims of inteinal cooiuinates

$(??YN#$ 8.A+5.4/3*

"nucchain" builus up the inteinal cooiuinates foi a nucleic aciu sequence fiom the sugai type,
backbone anu glycosiuic toisional values

$(?P&#? G+5X+;C

"nucleic" builus the inteinal anu Caitesian cooiuinates of a polynucleotiue fiom nucleic aciu
sequence anu toisional angle values foi the nucleic aciu backbone anu siue chains

$(OV&' >.364/53

"numbei" conveits a text numeial into an integei value; the input stiing must contain only numeiic
chaiacteis

$(O&'NP 8.A+5.4/3*

"numeial" conveits an input integei numbei into the coiiesponuing iight- oi left-justifieu text
numeial

$(O-'NI 8.A+5.4/3*

"numgiau" computes the giauient of the objective function "fvalue" with iespect to Caitesian
cooiuinates of the atoms via a two-siueu numeiical uiffeientiation

J?ZO 8.A+5.4/3*

"ocvm" is an optimally conuitioneu vaiiable metiic nonlineai optimization ioutine without line
seaiches

JPIN"O8.A+5.4/3*

"oluatm" get the Caitesian cooiuinates foi an atom fiom the Piotein Bata Bank file, then assigns the
atom type anu atomic connectivities

JG&$&$I 8.A+5.4/3*

"openenu" opens a file on a Foitian unit such that the position is set to the bottom foi appenuing to
the enu of the file
117 "#$%&' ()*+,) -./0* 117

JG"#O#S1 >.364/53

"optimiz1" is a seivice ioutine that computes the eneigy anu giauient foi optimally conuitioneu
vaiiable metiic optimization in Caitesian cooiuinate space

JG"#O#S& G+5X+;C

"optimize" peifoims eneigy minimization in Caitesian cooiuinate space using an optimally
conuitioneu vaiiable metiic methou

JG"#'J" G+5X+;C

"optiiot" peifoims an eneigy minimization in toisional angle space using an optimally conuitioneu
vaiiable metiic methou

JG"#'J"1 >.364/53

"optiiot1" is a seivice ioutine that computes the eneigy anu giauient foi optimally conuitioneu
vaiiable metiic optimization in toisional angle space

JG"'#-#I G+5X+;C

"optiigiu" peifoims an eneigy minimization of iigiu bouy atom gioups using an optimally
conuitioneu vaiiable metiic methou

JG"'#-#I1 >.364/53

"optiigiu1" is a seivice ioutine that computes the eneigy anu giauient foi optimally conuitioneu
vaiiable metiic optimization of iigiu bouies

JG"8NZ& 8.A+5.4/3*

"optsave" is useu by the optimizeis to wiite imteimeuiate cooiuinates anu othei ielevant
infoimation; also checks foi usei iequesteu teimination of an optimization

J'V#"NP 8.A+5.4/3*

"oibital" finus anu oiganizes lists of atoms in a pisystem, bonus connecting pisystem atoms anu
toisions whose two cential atoms aie both pisystem atoms

J'#&$" 8.A+5.4/3*

"oiient" computes a set of iefeience Caitesian cooiuinates in stanuaiu oiientation foi each iigiu
bouy atom gioup

J'"YJ- 8.A+5.4/3*

"oithog" peifoims an oithogonalization of an input matiix via the mouifieu uiam-Schmiut algoiithm
118 "#$%&' ()*+,) -./0* 118

JZ&'PNG 8.A+5.4/3*

"oveilap" computes the oveilap foi two paiallel p-oibitals given the atomic numbeis anu uistance of
sepaiation

GN'NORS& 8.A+5.4/3*

"paiamyze" piints the foice fielu paiameteis useu in the computation of each of the potential eneigy
teims

GN88V 8.A+5.4/3*

GN88VD 8.A+5.4/3*

GN88VL 8.A+5.4/3*

GN88VW 8.A+5.4/3*

GN88V[ 8.A+5.4/3*

GN88> 8.A+5.4/3*

GN88>D 8.A+5.4/3*

GN88>L 8.A+5.4/3*

GN88>W 8.A+5.4/3*

GN88>[ 8.A+5.4/3*

GN"Y G+5X+;C

"path" locates a seiies of stiuctuies equally spaceu along a confoimational pathway connecting the
input ieactant anu piouuct stiuctuies; a seiies of constiaineu optimizations oithogonal to the path is
uone via Lagiangian multiplieis

GN"Y1 >.364/53

GN"YG$" 8.A+5.4/3*

"pathpnt" finus a stiuctuie on the synchionous tiansit path with the specifieu path value "t"

GN"Y8?N$ 8.A+5.4/3*

"pathscan" makes a scan of a synchionous tiansit pathway by computing stiuctuies anu eneigies foi
specific path values

GN"YZNP 8.A+5.4/3*
119 "#$%&' ()*+,) -./0* 119

"pathval" computes the synchionous tiansit path value foi the specifieu stiuctuie

GIVN"O 8.A+5.4/3*

"pubatm" auus an atom to the Piotein Bata Bank file

GIVQRS G+5X+;C

"pubxyz" takes as input a Piotein Bata Bank file anu then conveits to anu wiites out a Caitesian
cooiuinates file anu, foi biopolymeis, a sequence file

G#NP"&' 8.A+5.4/3*

"pialtei" fiist mouifies bonu lengths anu foice constants accoiuing to the stanuaiu bonu slope
paiameteis anu the bonu oiuei values stoieu in "pnpl"; also alteis some 2-folu toisional paiameteis
baseu on the bonu-oiuei * beta matiix

G#OJZ& 8.A+5.4/3*

"pimove" iotates the vectoi between atoms "list(1)" anu "list(2)" so that atom 1 is at the oiigin anu
atom 2 along the x-axis; the atoms uefining the iespective planes aie also moveu anu theii bonu
lengths noimalizeu

G#GPN$& 8.A+5.4/3*

"piplane" selects the thiee atoms which specify the plane peipenuiculai to each p-oibital; the cuiient
veision will fail in ceitain situations, incluuing ketenes, allenes, anu isolateu oi aujacent tiiple bonus

G#8?> 8.A+5.4/3*

"piscf" peifoims an scf moleculai oibital calculation foi the pisystem using a mouifieu Paiisei-Paii-
Pople methou

G#"#P" 8.A+5.4/3*

"pitilt" calculates foi each pibonu the iatio of the actual p-oibital oveilap integial to the iueal oveilap
if the same oibitals weie peifectly paiallel

GPN?& 8.A+5.4/3*

"place" finus the piobe sites by putting the piobe spheie tangent to each tiiple of neighboiing atoms

GJPN'-'G 8.A+5.4/3*

"polaigip" geneiates membeis of the polaiization gioup of each atom anu sepaiate lists of the 1-2, 1-
S anu 1-4 gioup connectivities

GJPN'#S& G+5X+;C
120 "#$%&' ()*+,) -./0* 120

"polaiize" computes the moleculai polaiizability by applying an exteinal fielu along each axis
followeu by uiagonalization of the iesulting polaiizability tensoi

GJPRO&' 8.A+5.4/3*

"polymei" tests foi the piesence of an infinite polymei extenuing acioss peiiouic bounuaiies

GJPRG 8.A+5.4/3*

"polyp" is a polynomial piouuct ioutine that multiplies two algebiaic foims

GJ"$'- >.364/53

GJ"J>> 8.A+5.4/3*

"potoff" cleais the foicefielu uefinition by tuining off the use of each of the potential eneigy functions

GJ<&' 8.A+5.4/3*

"powei" uses the powei methou with ueflation to compute the few laigest eigenvalues anu
eigenvectois of a symmetiic matiix

G'&?#8& >.364/53

"piecise" finus a machine piecision value as selecteu by the input aigument: (1) the smallest positive
floating point value, (2) the smallest ielative floating point spacing, (S) the laigest ielative floating
point spacing

G'&?J$I 8.A+5.4/3*

"pieconu" solves a simplifieu veision of the Newton equations Ns = i, anu uses the iesult to
pieconuition lineai conjugate giauient iteiations on the full Newton equations in "tnsolve"

G'&88('& 8.A+5.4/3*

"piessuie" uses the inteinal viiial to finu the piessuie in a peiiouic box anu maintains a constant
uesiieu piessuie by scaling the cooiuinates via coupling to an exteinal constant piessuie bath

G'O%&R 8.A+5.4/3*

"fielu" paises a text stiing to extiact keywoius ielateu to foice fielu potential eneigy functional foims
anu constants

G'J?YN#$ 8.A+5.4/3*

"piochain" builus up the inteinal cooiuinates foi an amino aciu sequence fiom the phi, psi, omega
anu chi values

121 "#$%&' ()*+,) -./0* 121
G'Je?" 8.A+5.4/3*

G'JOJ 8.A+5.4/3*

"piomo" wiites a shoit message containing infoimation about the TINKER veision numbei anu the
copyiight notice

G'JG&'"R >.364/53

"piopeity" takes two input snapshot fiames anu computes the value of the piopeity foi which the
coiielation function is being accumulateu

G'JGRS& 8.A+5.4/3*

"piopyze" finus anu piints the total chaige, uipole moment components, iauius of gyiation anu
moments of ineitia

G'J8#I& 8.A+5.4/3*

"piosiue" builus the siue chain foi a single amino aciu iesiuue in teims of inteinal cooiuinates

G'J"&#$ G+5X+;C

"piotein" builus the inteinal anu Caitesian cooiuinates of a polypeptiue fiom amino aciu sequence
anu toisional angle values foi the peptiue backbone anu siue chains

G'"N'? 8.A+5.4/3*

"pitaic" wiites out a set of Caitesian cooiuinates foi all active atoms in the TINKER XYZ aichive
foimat

G'"?N' 8.A+5.4/3*

"pitcai" wiites out a set of Caitesian cooiuinates foi all active atoms in the Acceleiys InsightII .cai
foimat

G'"IR$ 8.A+5.4/3*

"pituyn" wiites out the infoimation neeueu to iestait a moleculai uynamics tiajectoiy to an exteinal
uisk file

G'"&'' 8.A+5.4/3*

"piteii" wiites out a set of cooiuinates to a uisk file piioi to aboiting on a seiious eiioi

G'"#$" 8.A+5.4/3*

"pitint" wiites out a set of Z-matiix inteinal cooiuinates to an exteinal uisk file

122 "#$%&' ()*+,) -./0* 122
G'"OJPD G+5X+;C

"pitmol2" wiites out a set of cooiuinates in Sybyl N0L2 foimat to an exteinal uisk file

G'"GIV 8.A+5.4/3*

"pitpub" wiites out a set of Piotein Bata Bank cooiuinates to an exteinal uisk file

G'"G'O 8.A+5.4/3*

"pitpim" wiites out a foimatteu listing of the uefault set of potential eneigy paiameteis foi a foice
fielu

G'"8&K 8.A+5.4/3*

"pitseq" wiites out a biopolymei sequence to an exteinal uisk file with 1S iesiuues pei line anu
uistinct chains sepaiateu by blank lines

G'"QOJP 8.A+5.4/3*

"pitxmol" wiites out a set of Caitesian cooiuinates foi all active atoms in a simple, geneiic XYZ
foimat oiiginally useu by the XN0L piogiam

G'"QRS 8.A+5.4/3*

"pitxyz" wiites out a set of Caitesian cooiuinates to an exteinal uisk file

G88 G+5X+;C

"pss" implements the potential smoothing plus seaich methou foi global optimization in Caitesian
cooiuinate space with local seaiches peifoimeu in Caitesian oi toisional space

G881 >.364/53

"pss1" is a seivice ioutine that computes the eneigy anu giauient uuiing PSS global optimization in
Caitesian cooiuinate space

G88D 8.A+5.4/3*

"pss2" is a seivice ioutine that computes the spaise matiix Bessian elements uuiing PSS global
optimization in Caitesian cooiuinate space

G88'-I1 >.364/53

"pssigu1" is a seivice ioutine that computes the eneigy anu giauient uuiing PSS global optimization
ovei iigiu bouies

G88'#-#I G+5X+;C

123 "#$%&' ()*+,) -./0* 123
"pssiigiu" implements the potential smoothing plus seaich methou foi global optimization foi a set of
iigiu bouies

G88'J" G+5X+;C

"pssiot" implements the potential smoothing plus seaich methou foi global optimization in toisional
space

G88'J"1 >.364/53

"pssiot1" is a seivice ioutine that computes the eneigy anu giauient uuiing PSS global optimization
in toisional space

G88<'#"& 8.A+5.4/3*

G"#$?R >.364/53

GS&Q"' 8.A+5.4/3*

"pzexti" is a polynomial extiapolation ioutine useu uuiing Buliisch-Stoei integiation of oiuinaiy
uiffeiential equations

K'>N?" 8.A+5.4/3*

"qifact" peifoims Bouseholuei tiansfoimations with column pivoting (optional) to compute a QR
factoiization of the m by n matiix a; the ioutine ueteimines an oithogonal matiix q, a peimutation
matiix p, anu an uppei tiapezoiual matiix i with uiagonal elements of nonincieasing magnituue, such
that a*p = q*i; the Bouseholuei tiansfoimation foi column k, k = 1,2,...,min(m,n), is of the foim

K'8JPZ& 8.A+5.4/3*

"qisolve" solves a*x=b anu u*x=u in the least squaies sense; noimally useu in combination with
ioutine "qifact" to solve least squaies pioblems

K(N">#" 8.A+5.4/3*

"quatfit" uses a quateinion-baseu methou to achieve the best fit supeiposition of two sets of
cooiuinates

'NI#NP G+5X+;C

"iauial" finus the iauial uistiibution function foi a specifieu paii of atom types via analysis of a set of
cooiuinate fiames

'N$IJO >.364/53

"ianuom" geneiates a ianuom numbei on |u,1j via a long peiiou geneiatoi uue to L'Ecuyei with
Bays-Buiham shuffle

'N$Z&? 8.A+5.4/3*
124 "#$%&' ()*+,) -./0* 124

"ianvec" geneiates a unit vectoi in S-uimensional space with unifoimly uistiibuteu ianuom
oiientation

'N""P& 8.A+5.4/3*

"iattle" implements the fiist poition of the iattle algoiithm by coiiecting atomic positions anu half-
step velocities to maintain inteiatomic uistance anu absolute spatial constiaints

'N""P&D 8.A+5.4/3*

"iattle2" implements the seconu poition of the iattle algoiithm by coiiecting the full-step velocities
in oiuei to maintain inteiatomic uistance constiaints

'&NIVP% 8.A+5.4/3*

"ieaublk" ieaus in a set of snapshot fiames anu tiansfeis the values to inteinal aiiays foi use in the
computation of time coiielation functions

'&NIIR$ 8.A+5.4/3*

"ieauuyn" get the positions, velocities anu acceleiations foi a moleculai uynamics iestait fiom an
exteinal uisk file

'&NI#$" 8.A+5.4/3*

"ieauint" gets a set of Z-matiix inteinal cooiuinates fiom an exteinal file

'&NIOJPD 8.A+5.4/3*

"ieaumol2" gets a set of Sybyl N0L2 cooiuinates fiom an exteinal uisk file

'&NIGIV 8.A+5.4/3*

"ieaupub" gets a set of Piotein Bata Bank cooiuinates fiom an exteinal uisk file

'&NIG'O 8.A+5.4/3*

"ieaupim" piocesses the potential eneigy paiametei file in oiuei to uefine the uefault foice fielu
paiameteis

'&NI8&K 8.A+5.4/3*

"ieauseq" gets a biopolymei sequence containing one oi moie sepaiate chains fiom an exteinal file;
all lines containing sequence must begin with the staiting sequence numbei, the actual sequence is
ieau fiom subsequent nonblank chaiacteis

'&NIQRS 8.A+5.4/3*

125 "#$%&' ()*+,) -./0* 125
"ieauxyz" gets a set of Caitesian cooiuinates fiom an exteinal uisk file

'&>#$& 8.A+5.4/3*

"iefine" peifoims minimization of the atomic cooiuinates of an initial ciuue embeuueu uistance
geometiy stiuctuie veisus the bounu, chiiality, planaiity anu toisional eiioi functions

'&P&N8&OJ$#"J' 8.A+5.4/3*

'&GP#?N 8.A+5.4/3*

"ieplica" ueciues between images anu ieplicates foi geneiation of peiiouic bounuaiy conuitions, anu
sets the cell ieplicate list if the ieplicates methou is to be useu

'>#$I&Q 8.A+5.4/3*

"ifinuex" finus inuices foi each multipole site foi use in computing ieaction fielu eneigetics

'-I8'?Y 8.A+5.4/3*

'-I8"&G 8.A+5.4/3*

"igustep" peifoims a single moleculai uynamics time step foi a iigiu bouy calculation

'#VJ8JO& 8.A+5.4/3*

"iibosome" tianslates a polypeptiue stiuctuie in Piotein Bata Bank foimat to a Caitesian cooiuinate
file anu sequence file

'#-#IQRS 8.A+5.4/3*

"iigiuxyz" computes Caitesian cooiuinates foi a iigiu bouy gioup via iotation anu tianslation of
iefeience cooiuinates

'#$-8 8.A+5.4/3*

"iings" seaiches the stiuctuie foi small iings anu stoies theii constituent atoms

'O8&''J' 8.A+5.4/3*

"imseiioi" computes the maximum absolute ueviation anu the ims ueviation fiom the uistance
bounus, anu the numbei anu ims value of the uistance iestiaint violations

'O8>#" >.364/53

"imsfit" computes the ims fit of two cooiuinate sets

'J"N$- >.364/53

126 "#$%&' ()*+,) -./0* 126
'J"?Y&?% >.364/53

"iotcheck" tests a specifieu canuiuate iotatable bonu foi the uisalloweu case wheie inactive atoms
aie founu on both siues of the canuiuate bonu

'J"&(P&' 8.A+5.4/3*

"ioteulei" computes a set of Eulei angle values consistent with an input iotation matiix

'J"P#8" 8.A+5.4/3*

"iotlist" geneiates the minimum list of all the atoms lying to one siue of a paii of uiiectly bonueu
atoms; optionally finus the minimal list by choosing the siue with fewei atoms

'J"ON" 8.A+5.4/3*

"iotmat" finus the iotation matiix that conveits fiom the local cooiuinate system to the global fiame
at a multipole site

'J"GJP& 8.A+5.4/3*

"iotpole" constiucts the set of atomic multipoles in the global fiame by applying the coiiect iotation
matiix foi each site

'J"'-I 8.A+5.4/3*

"iotigu" finus the iotation matiix foi a iigiu bouy uue to a single step of uynamics

'J"8#"& 8.A+5.4/3*

"iotsite" computes the atomic multipoles at a specifieu site in the global cooiuinate fiame by
applying a iotation matiix

8NIIP& G+5X+;C

"sauule" finus a tiansition state between two confoimational minima using a combination of iueas
fiom the synchionous tiansit (Balgien-Lipscomb) anu quauiatic path (Bell-Ciighton) methous

8NIIP&1 >.364/53

"sauule1" is a seivice ioutine that computes the eneigy anu giauient foi tiansition state optimization

8NIIP&8 8.A+5.4/3*

"sauules" constiucts ciicles, convex euges anu sauule faces

8?N$ G+5X+;C

127 "#$%&' ()*+,) -./0* 127
"scan" attempts to finu all the local minima on a potential eneigy suiface via an iteiative seiies of
local seaiches

8?N$1 >.364/53

"scan1" is a seivice ioutine that computes the eneigy anu giauient uuiing exploiation of a potential
eneigy suiface via iteiative local seaich

8?N$D 8.A+5.4/3*

"scan2" is a seivice ioutine that computes the spaise matiix Bessian elements uuiing exploiation of
a potential eneigy suiface via iteiative local seaich

8IN'&N 8.A+5.4/3*

"suaiea" optionally scales the atomic fiiction coefficient of each atom baseu on its accessible suiface
aiea

8I8"&G 8.A+5.4/3*

"sustep" peifoims a single stochastic uynamics time step via a velocity veilet integiation algoiithm

8I"&'O 8.A+5.4/3*

"suteim" gets fiictional anu ianuom foice teims neeueu to upuate positions anu velocities via
stochastic uynamics

8&N'?Y 8.A+5.4/3*

"seaich" is a uniuimensional line seaich baseu upon paiabolic extiapolation anu cubic inteipolation
using both function anu giauient values; if foiceu to seaich in an uphill uiiection, ietuin is aftei the
initial step

8&"N??&P&'N"#J$ 8.A+5.4/3*

8&"N"JO#? 8.A+5.4/3*

8&"N"JO"RG&8 8.A+5.4/3*

8&"?YN'-& 8.A+5.4/3*

8&"?J$$&?"#Z#"R 8.A+5.4/3*

8&"?JJ'I#$N"&8 8.A+5.4/3*

8&"&$&'-R 8.A+5.4/3*

8&">#P& 8.A+5.4/3*

128 "#$%&' ()*+,) -./0* 128
8&">J'?&>#&PI 8.A+5.4/3*

8&"-'NI#&$"8 8.A+5.4/3*

8&"#O& 8.A+5.4/3*

"setime" initializes the elapseu inteival CP0 timei

8&"#$I(?&I 8.A+5.4/3*

8&"%&R<J'I 8.A+5.4/3*

8&"ON88 8.A+5.4/3*

8&"$NO& 8.A+5.4/3*

8&"8"&G 8.A+5.4/3*

8&"8"J'R 8.A+5.4/3*

8&""#O& 8.A+5.4/3*

8&"(GIN"&I 8.A+5.4/3*

8&"Z&PJ?#"R 8.A+5.4/3*

8YN%&(G 8.A+5.4/3*

"shakeup" initializes any holonomic constiaints foi use with the iattle algoiithm uuiing moleculai
uynamics

8#-OJ#I >.364/53

"sigmoiu" implements a noimalizeu sigmoiual function on the inteival |u,1j; the cuives connect (u,u)
to (1,1) anu have a coopeiativity contiolleu by beta, they appioach a stiaight line as beta -> u anu get
moie nonlineai as beta incieases

8%"IR$ 8.A+5.4/3*

"sktuyn" senus the cuiient uynamics info via a socket

8%"#$#" 8.A+5.4/3*

"sktinit" sets up socket communication with the giaphical usei inteiface by staiting a }ava viitual
machine, initiating a seivei, anu loauing an object with system infoimation

8%"%#PP 8.A+5.4/3*

"sktkill" closes the seivei anu }ava viitual machine
129 "#$%&' ()*+,) -./0* 129

8%"JG" 8.A+5.4/3*

"sktopt" senus the cuiient optimization info via a socket

8PN"&' 8.A+5.4/3*

"slatei" is a geneial ioutine foi computing the oveilap integials between two Slatei-type oibitals

8OJJ"Y 8.A+5.4/3*

"smooth" sets the type of smoothing methou anu the extent of suiface uefoimation foi use with
potential eneigy smoothing

8$#>>&' G+5X+;C

"sniffei" peifoims a global eneigy minimization using a uisciete veision of uiiewank's global seaich
tiajectoiy

8$#>>&'1 >.364/53

"sniffei1" is a seivice ioutine that computes the eneigy anu giauient foi the Sniffei global
optimization methou

8JN% 8.A+5.4/3*

"soak" takes a cuiiently uefineu solute system anu places it into a solvent box, with iemoval of any
solvent molecules that oveilap the solute

8J'" 8.A+5.4/3*

"soit" takes an input list of integeis anu soits it into ascenuing oiuei using the Beapsoit algoiithm

8J'"1T 8.A+5.4/3*

"soit1u" takes an input list of chaiactei stiings anu soits it into alphabetical oiuei using the Beapsoit
algoiithm, uuplicate values aie iemoveu fiom the final soiteu list

8J'"D 8.A+5.4/3*

"soit2" takes an input list of ieals anu soits it into ascenuing oiuei using the Beapsoit algoiithm; it
also ietuins a key into the oiiginal oiueiing

8J'"L 8.A+5.4/3*

"soitS" takes an input list of integeis anu soits it into ascenuing oiuei using the Beapsoit algoiithm;
it also ietuins a key into the oiiginal oiueiing

8J'"W 8.A+5.4/3*
130 "#$%&' ()*+,) -./0* 130

"soit4" takes an input list of integeis anu soits it into ascenuing absolute value using the Beapsoit
algoiithm

8J'"[ 8.A+5.4/3*

"soitS" takes an input list of integeis anu soits it into ascenuing oiuei baseu on each value mouulo
"m"

8J'"] 8.A+5.4/3*

"soit6" takes an input list of chaiactei stiings anu soits it into alphabetical oiuei using the Beapsoit
algoiithm

8J'"_ 8.A+5.4/3*

"soit7" takes an input list of chaiactei stiings anu soits it into alphabetical oiuei using the Beapsoit
algoiithm; it also ietuins a key into the oiiginal oiueiing

8J'"h 8.A+5.4/3*

"soit8" takes an input list of integeis anu soits it into ascenuing oiuei using the Beapsoit algoiithm,
uuplicate values aie iemoveu fiom the final soiteu list

8J'"i 8.A+5.4/3*

"soit9" takes an input list of ieals anu soits it into ascenuing oiuei using the Beapsoit algoiithm,
uuplicate values aie iemoveu fiom the final soiteu list

8GN?&>#PP G+5X+;C

"spacefill" computes the suiface aiea anu volume of a stiuctuie; the van uei Waals, accessible-
excluueu, anu contact-ieentiant uefinitions aie available

8G&?"'(O G+5X+;C

"spectium" computes a powei spectium ovei a wavelength iange fiom the velocity autocoiielation
as a function of time

8K(N'& 8.A+5.4/3*

"squaie" is a nonlineai least squaies ioutine ueiiveu fiom the INSL ioutine BCLSF anu Noie's
Ninpack ioutine LNBER; the }acobian is estimateu by finite uiffeiences anu bounus can be specifieu
foi the vaiiables to be iefineu

8(>>#Q 8.A+5.4/3*

"suffix" checks a filename foi the piesence of an extension, anu appenus an extension if none is founu

8(G&'GJ8& G+5X+;C
131 "#$%&' ()*+,) -./0* 131

"supeipose" takes paiis of stiuctuies anu supeiimposes them in the optimal least squaies sense; it
will attempt to match all atom paiis oi only those specifieu by the usei

8('>N?& 8.A+5.4/3*

"suiface" peifoims an analytical computation of the weighteu solvent accessible suiface aiea of each
atom anu the fiist ueiivatives of the aiea with iespect to Caitesian cooiuinates

8('>N"JO 8.A+5.4/3*

"suifatom" peifoims an analytical computation of the suiface aiea of a specifieu atom; a simplifieu
veision of "suiface"

8<#"?Y 8.A+5.4/3*

"switch" sets the coeffcients useu by the fifth anu seventh oiuei polynomial switching functions foi
spheiical cutoffs

8RVRPQRS G+5X+;C

"sybylxyz" takes as input a Sybyl N0L2 cooiuinates file, conveits to anu then wiites out Caitesian
cooiuinates

8ROO&"'R 8.A+5.4/3*

"symmetiy" applies symmetiy opeiatois to the fiactional cooiuinates of the asymmetiic unit in
oiuei to geneiate the symmetiy ielateu atoms of the full unit cell

"N$-&$" 8.A+5.4/3*

"tangent" finus the piojecteu giauient on the synchionous tiansit path foi a point along the tiansit
pathway

"&OG&' 8.A+5.4/3*

"tempei" applies a velocity coiiection at the half time step as neeueu foi the Nose-Boovei extenueu
system theimostat

"&OG&'D 8.A+5.4/3*

"tempei2" computes the instantaneous tempeiatuie anu applies a theimostat via Beienusen velocity
scaling, Anueisen stochastic collisions, Langevin piston oi Nose-Boovei extenueu systems

"&8"-'NI G+5X+;C

"testgiau" computes anu compaies the analytical anu numeiical giauient vectois of the potential
eneigy function with iespect to Caitesian cooiuinates

"&8"Y&88 G+5X+;C
132 "#$%&' ()*+,) -./0* 132

"testhess" computes anu compaies the analytical anu numeiical Bessian matiices of the potential
eneigy function with iespect to Caitesian cooiuinates

"&8"P#-Y" G+5X+;C

"testlight" peifoims a set of timing tests to compaie the evaluation of potential eneigy anu
eneigygiauient using the methou of lights with a uouble loop ovei all atom paiis

"&8"'J" G+5X+;C

"testiot" computes anu compaies the analytical anu numeiical giauient vectois of the potential
eneigy function with iespect to iotatable toisional angles

"#O&' G+5X+;C

"timei" measuies the CP0 time iequiieu foi file ieauing anu paiametei assignment, potential eneigy
computation, eneigy anu giauient computation, anu Bessian matiix evaluation

"#O&'J" G+5X+;C

"timeiot" measuies the CP0 time iequiieu foi file ieauing anu paiametei assignment, potential
eneigy computation, eneigy anu giauient ovei toisions, anu toisional angle Bessian matiix
evaluation

"$?- 8.A+5.4/3*

"tncg" implements a tiuncateu Newton optimization algoiithm in which a pieconuitioneu lineai
conjugate giauient methou is useu to appioximately solve Newton's equations; special featuies
incluue use of an explicit spaise Bessian oi finite-uiffeience giauient-Bessian piouucts within the
PCu iteiation; the exact Newton seaich uiiections can be useu optionally; by uefault the algoiithm
checks foi negative cuivatuie to pievent conveigence to a stationaiy point having negative
eigenvalues; if a sauule point is uesiieu this test can be iemoveu by uisabling "negtest"

"$8JPZ& 8.A+5.4/3*

"tnsolve" uses a lineai conjugate giauient methou to finu an appioximate solution to the set of lineai
equations iepiesenteu in matiix foim by Bp = -g (Newton's equations)

"J'GYN8& 8.A+5.4/3*

"toiphase" sets the n-folu amplituue anu phase values foi each toision via soiting of the input
paiameteis

"J'K(& 8.A+5.4/3*

"toique" takes the toique values on sites uefineu by local cooiuinate fiames anu uistiibutes thme to
conveit to foices on the oiiginal sites anu sites specifying the local fiames

"J'K(&1 8.A+5.4/3*
133 "#$%&' ()*+,) -./0* 133

"toique1" takes the toique value on a site uefineu by a local cooiuinate fiame anu uistiibutes it to
conveit to foices on the oiiginal site anu sites specifying the local fiame

"J'8&' >.364/53

"toisei" computes the toisional eiioi function anu its fiist ueiivatives with iespect to the atomic
Caitesian cooiuinates baseu on the ueviation of specifieu toisional angles fiom uesiieu values, the
containeu bonu angles aie also iestiaineu to avoiu a numeiical instability

"J'8#J$8 8.A+5.4/3*

"toisions" finus the total numbei of uiheuial angles anu the numbeis of the foui atoms uefining each
uiheuial angle

"J'(8 8.A+5.4/3*

"toius" sets a list of all of the tempoiaiy toius positions by testing foi a toius between each atom anu
its neighbois

"J"&'' >.364/53

"toteii" is the eiioi function anu ueiivatives foi a uistance geometiy embeuuing; it incluues
components fiom the uistance bounus, haiu spheie contacts, local geometiy, chiiality anu toisional
iestiaint eiiois

"'N$8#" >.364/53

"tiansit" evaluates the synchionous tiansit function anu giauient; lineai anu quauiatic tiansit paths
aie available

"'#N$-P& 8.A+5.4/3*

"tiiangle" smooths the uppei anu lowei uistance bounus via the tiiangle inequality using a full-
matiix vaiiant of the Floyu-Waishall shoitest path algoiithm; this ioutine is usually much slowei
than the spaise matiix shoitest path methous in "geouesic" anu "tiifix", anu shoulu be useu only foi
compaiison with answeis geneiateu by those ioutines

"'#>#Q 8.A+5.4/3*

"tiifix" iebuilus both the uppei anu lowei uistance bounu matiices following tightening of one oi
both of the bounus between a specifieu paii of atoms, "p" anu "q", using a mouification of
Nuichlanu's shoitest path upuate algoiithm

"'#O"&Q" >.364/53

"tiimtext" finus anu ietuins the location of the last non-blank chaiactei befoie the fiist null chaiactei
in an input text stiing; the function ietuins zeio if no such chaiactei is founu

"'#GP& >.364/53
134 "#$%&' ()*+,) -./0* 134

"tiiple" finus the tiiple piouuct of thiee vectois; useu as a seivice ioutine by the Connolly suiface
aiea anu volume computation

"'(8" 8.A+5.4/3*

"tiust" upuates the mouel tiust iegion foi a nonlineai least squaies calculation; this veision is baseu
on the iueas founu in NL2S0L anu in Bennis anu Schnabel's book

(I#'&?"1 8.A+5.4/3*

"uuiiect1" computes the iecipiocal space contiibution of the peimanent atomic multipole moments
to the electiostatic fielu foi use in finuing the uiiect inuuceu uipole moments via a iegulai Ewalu
summation

(I#'&?"D 8.A+5.4/3*

"uuiiect2" computes the ieal space contiibution of the peimanent atomic multipole moments to the
electiostatic fielu foi use in finuing the uiiect inuuceu uipole moments via a iegulai Ewalu
summation

(>#&PI 8.A+5.4/3*

"ufielu" finus the fielu at each polaiizable site uue to the inuuceu uipoles at the othei sites using
Thole's methou to uamp the fielu at close iange

(O("(NP1 8.A+5.4/3*

"umutual1" computes the iecipiocal space contiibution of the inuuceu atomic uipole moments to the
electiostatic fielu foi use in iteiative calculation of inuuceu uipole moments via a iegulai Ewalu
summation

(O("(NPD 8.A+5.4/3*

"umutual2" computes the ieal space contiibution of the inuuceu atomic uipole moments to the
electiostatic fielu foi use in iteiative calculation of inuuceu uipole moments via a iegulai Ewalu
summation

($#"?&PP 8.A+5.4/3*

"unitcell" gets the peiiouic bounuaiy box size anu ielateu values fiom an exteinal keywoiu file

(G?N8& 8.A+5.4/3*

"upcase" conveits a text stiing to all uppei case letteis

ZNO 8.A+5.4/3*

"vam" takes the analytical moleculai suiface uefineu as a collection of spheiical anu toioiual
polygons anu uses it to compute the volume anu suiface aiea
135 "#$%&' ()*+,) -./0* 135

Z?'J88 8.A+5.4/3*

"vcioss" finus the cioss piouuct of two vectois

ZI<&'' >.364/53

"vuweii" is the haiu spheie van uei Waals bounu eiioi function anu ueiivatives that penalizes close
nonbonueu contacts, paiiwise neighbois aie geneiateu via the methou of lights

Z&?N$- >.364/53

"vecang" finus the angle between two vectois hanueu with iespect to a cooiuinate axis; ietuins an
angle in the iange |u,2*pij

Z&'P&" 8.A+5.4/3*

"veilet" peifoims a single moleculai uynamics time step by means of the velocity veilet multistep
iecuision foimula

Z&'8#J$ 8.A+5.4/3*

"veision" checks the name of a file about to be openeu; if if "olu" status is passeu, the name of the
highest cuiient veision is ietuineu; if "new" status is passeu the filename of the next available
unuseu veision is geneiateu

Z#V'N"& G+5X+;C

"vibiate" peifoims a vibiational noimal moue analysis; the Bessian matiix of seconu ueiivatives is
ueteimineu anu then uiagonalizeu both uiiectly anu aftei mass weighting; output consists of the
eigenvalues of the foice constant matiix as well as the vibiational fiequencies anu uisplacements

Z#V'#-#I G+5X+;C

"vibiigiu" computes the eigenvalues anu eigenvectois of the Bessian matiix ovei iigiu bouy uegiees
of fieeuom

Z#V'J" G+5X+;C

"vibiot" computes the eigenvalues anu eigenvectois of the toisional Bessian matiix

Z$J'O 8.A+5.4/3*

"vnoim" noimalizes a vectoi to unit length; useu as a seivice ioutine by the Connolly suiface aiea
anu volume computation

ZJP(O& 8.A+5.4/3*

"volume" calculates the excluueu volume via the Connolly analytical volume anu suiface aiea
algoiithm
136 "#$%&' ()*+,) -./0* 136

ZJP(O&1 8.A+5.4/3*

"volume1" calculates fiist ueiivatives of the total excluueu volume with iespect to the Caitesian
cooiuinates of each atom

ZJP(O&D 8.A+5.4/3*

"volume2" calculates seconu ueiivatives of the total excluueu volume with iespect to the Caitesian
cooiuinates of the atoms

<N"8J$ 8.A+5.4/3*

"watson" uses a iigiu bouy optimization to appioximately align the paiieu stianus of a nucleic aciu
uouble helix

<N"8J$1 >.364/53

"watson1" is a seivice ioutine that computes the eneigy anu giauient foi optimally conuitioneu
vaiiable metiic optimization of iigiu bouies

Q"NP&'' 8.A+5.4/3*

"xtaleii" computes an eiioi function value ueiiveu fiom ueiivatives with iespect to lattice
paiameteis, lattice eneigy anu monomei uipole moments

Q"NP>#" G+5X+;C

"xtalfit" computes an optimizeu set of potential eneigy paiameteis foi usei specifieu van uei Waals
anu electiostatic inteiactions by fitting to ciystal stiuctuie, lattice eneigy anu monomei uipole
moment uata

Q"NPPN"1 >.364/53

"xtalmol1" is a seivice ioutine that computes the eneigy anu numeiical giauient with iespect to the
six lattice lengths anu angles foi a ciystal eneigy minimization

Q"NPO#$ G+5X+;C

"xtalmin" peifoims a full ciystal eneigy minimization by alteinating cycles of tiuncateu Newton
optimization ovei atomic cooiuinates with vaiiable metiic optimization ovei the six lattice
uimensions anu angles

Q"NPOJP1 >.364/53

"xtalmol1" is a seivice ioutine that computes the eneigy anu giauient with iespect to the atomic
Caitesian cooiuinates foi a ciystal eneigy minimization

Q"NPOJPD 8.A+5.4/3*

137 "#$%&' ()*+,) -./0* 137
"xtalmol2" is a seivice ioutine that computes the spaise matiix Bessian elements with iespect to the
atomic Caitesian cooiuinates foi a ciystal eneigy minimization

Q"NPOJZ& 8.A+5.4/3*

"xtalmove" conveits fiactional to Caitesian cooiuinates foi iigiu molecules uuiing fitting of foice
fielu paiameteis to ciystal stiuctuie uata

Q"NPG'O 8.A+5.4/3*

"xtalpim" stoies oi ietiieves a ciystal stiuctuie; useu to make a pieviously stoieu stiuctuie the
cuiiently active stiuctuie, oi to stoie a stiuctuie foi latei use; only pioviues foi the inteimoleculai
eneigy teims

Q"NP<'" 8.A+5.4/3*

"xtalwit" is a utility that piints inteimeuiate iesults uuiing fitting of foice fielu paiameteis to ciystal
uata

QRSN"O 8.A+5.4/3*

"xyzatm" computes the Caitesian cooiuinates of a single atom fiom its uefining inteinal cooiuinate
values

QRS&I#" G+5X+;C

"xyzeuit" pioviues foi mouification anu manipulation of the contents of a Caitesian cooiuinates file

QRS#$" G+5X+;C

"xyzint" takes as input a Caitesian cooiuinates file, then conveits to anu wiites out an inteinal
cooiuinates file

QRSGIV G+5X+;C

"xyzpub" takes as input a Caitesian cooiuinates file, then conveits to anu wiites out a Piotein Bata
Bank file

QRS'#-#I 8.A+5.4/3*

"xyziigiu" computes the centei of mass anu Eulei angle iigiu bouy cooiuinates foi each atom gioup
in the system

QRS8RVRP G+5X+;C

"xyzsybyl" takes as input a Caitesian cooiuinates file, conveits to anu then wiites out a Sybyl N0L2
file

SN"JO 8.A+5.4/3*

138 "#$%&' ()*+,) -./0* 138
"zatom" auus an atom to the enu of the cuiient Z-matiix anu then inciements the atom countei; atom
type, uefining atoms anu inteinal cooiuinates aie passeu as aiguments

SY&PG 8.A+5.4/3*

"zhelp" piints the geneial infoimation anu instiuctions foi the Z-matiix euiting piogiam

SZNP(& 8.A+5.4/3*

"zvalue" gets usei supplieu values foi selecteu cooiuinates as neeueu by the inteinal cooiuinate
euiting piogiam

139 "#$%&' ()*+,) -./0* 139
1T2 I*)6+/@4/53) 59 -B5A;B Z;+/;AB*)
The Foitian common blocks founu in the TINKER package aie listeu below along with a biief
uesciiption of the contents of each vaiiable in each common block. Each inuiviuual common block is
piesent as a sepaiate ".i" file in the souice subuiiectoiy. A souice coue listing containing each of the
souice coue mouules anu each of the common blocks can be piouuceu by iunning the "listing.make"
sciipt founu in the uistiibution.

N?"#J$ 454;B 3.CA*+ 59 *;67 *3*+XE 4*+C 65C@.4*0

neb numbei of bonu stietch eneigy teims computeu
nea numbei of angle benu eneigy teims computeu
neba numbei of stietch-benu eneigy teims computeu
neub numbei of 0iey-Biauley eneigy teims computeu
neaa numbei of angle-angle eneigy teims computeu
neopb numbei of out-of-plane benu eneigy teims computeu
neopu numbei of out-of-plane uistance eneigy teims computeu
neiu numbei of impiopei uiheuial eneigy teims computeu
neit numbei of impiopei toision eneigy teims computeu
net numbei of toisional eneigy teims computeu
nept numbei of pi-oibital toision eneigy teims computeu
nebt numbei of stietch-toision eneigy teims computeu
nett numbei of toision-toision eneigy teims computeu
nev numbei of van uei Waals eneigy teims computeu
nec numbei of chaige-chaige eneigy teims computeu
necu numbei of chaige-uipole eneigy teims computeu
neu numbei of uipole-uipole eneigy teims computeu
nem numbei of multipole eneigy teims computeu
nep numbei of polaiization eneigy teims computeu
new numbei of Ewalu summation eneigy teims computeu
nei numbei of ieaction fielu eneigy teims computeu
nes numbei of solvation eneigy teims computeu
nelf numbei of metal liganu fielu eneigy teims computeu
neg numbei of geometiic iestiaint eneigy teims computeu
nex numbei of extia eneigy teims computeu

NP#-$ /395+C;4/53 95+ ).@*+@5)/4/53 59 )4+.64.+*)

wfit weights assigneu to atom paiis uuiing supeiposition
nfit numbei of atoms to use in supeiimposing two stiuctuies
ifit atom numbeis of paiis of atoms to be supeiimposeu

N$NPRS *3*+XE 65C@53*34) @;+4/4/53*0 5^*+ ;45C)

aesum total potential eneigy paititioneu ovei atoms
aeb bonu stietch eneigy paititioneu ovei atoms
aea angle benu eneigy paititioneu ovei atoms
aeba stietch-benu eneigy paititioneu ovei atoms
aeub 0iey-Biauley eneigy paititioneu ovei atoms
aeaa angle-angle eneigy paititioneu ovei atoms
aeopb out-of-plane benu eneigy paititioneu ovei atoms
140 "#$%&' ()*+,) -./0* 140
aeopu out-of-plane uistance eneigy paititioneu ovei atoms
aeiu impiopei uiheuial eneigy paititioneu ovei atoms
aeit impiopei toision eneigy paititioneu ovei atoms
aet toisional eneigy paititioneu ovei atoms
aept pi-oibital toision eneigy paititioneu ovei atoms
aebt stietch-toision eneigy paititioneu ovei atoms
aett toision-toision eneigy paititioneu ovei atoms
aev van uei Waals eneigy paititioneu ovei atoms
aec chaige-chaige eneigy paititioneu ovei atoms
aecu chaige-uipole eneigy paititioneu ovei atoms
aeu uipole-uipole eneigy paititioneu ovei atoms
aem multipole eneigy paititioneu ovei atoms
aep polaiization eneigy paititioneu ovei atoms
aei ieaction fielu eneigy paititioneu ovei atoms
aes solvation eneigy paititioneu ovei atoms
aelf metal liganu fielu eneigy paititioneu ovei atoms
aeg geometiic iestiaint eneigy paititioneu ovei atoms
aex extia eneigy teim paititioneu ovei atoms

N$-N$- ;3XB*`;3XB* 4*+C) /3 6.++*34 )4+.64.+*

kaa foice constant foi angle-angle cioss teims
nangang total numbei of angle-angle inteiactions
iaa angle numbeis useu in each angle-angle teim

N$-P& A530 ;3XB*) :/47/3 47* 6.++*34 )4+.64.+*

ak haimonic angle foice constant (kcalmoleiau**2)
anat iueal bonu angle oi phase shift angle (uegiees)
aflu peiiouicity foi Fouiiei bonu angle teim
nangle total numbei of bonu angles in the system
iang numbeis of the atoms in each bonu angle
angtyp potential eneigy function type foi each bonu angle

N$-GJ" )@*6/9/6) 59 A530 ;3XB* 9.364/53;B 95+C)

cang cubic coefficient in angle benuing potential
qang quaitic coefficient in angle benuing potential
pang quintic coefficient in angle benuing potential
sang sextic coefficient in angle benuing potential
angunit conveit angle benuing eneigy to kcalmole
stbnunit conveit stietch-benu eneigy to kcalmole
aaunit conveit angle-angle eneigy to kcalmole
opbunit conveit out-of-plane benu eneigy to kcalmole
opuunit conveit out-of-plane uistance eneigy to kcalmole
mm2stbn logical flag goveining use of NN2-style stietch-benu

N'-(& 65CC;30 B/3* ;+X.C*34) ;4 @+5X+;C )4;+4.@

maxaig maximum numbei of commanu line aiguments
naig numbei of commanu line aiguments to the piogiam
listaig flag to maik available commanu line aiguments
141 "#$%&' ()*+,) -./0* 141
aig stiings containing the commanu line aiguments

N"OP8" B56;B X*5C*4+E 4*+C) /3^5B^/3X *;67 ;45C

bnulist list of the bonu numbeis involving each atom
anglist list of the angle numbeis centeieu on each atom

N"O"RG ;45C/6 @+5@*+4/*) 95+ *;67 6.++*34 ;45C

mass atomic weight foi each atom in the system
tag integei atom labels fiom input cooiuinates file
class atom class numbei foi each atom in the system
atomic atomic numbei foi each atom in the system
valence valence numbei foi each atom in the system
name atom name foi each atom in the system
stoiy uesciiptive type foi each atom in system

N"JO8 3.CA*+U @5)/4/53 ;30 4E@* 59 6.++*34 ;45C)

x cuiient x-cooiuinate foi each atom in the system
y cuiient y-cooiuinate foi each atom in the system
z cuiient z-cooiuinate foi each atom in the system
n total numbei of atoms in the cuiient system
type atom type numbei foi each atom in the system

VN"Y 4*C@*+;4.+* ;30 @+*)).+* 6534+5B @;+;C*4*+)

maxnose maximum length of the Nose-Boovei chain
kelvinu taiget value foi the system tempeiatuie (K)
kelvin vaiiable taiget tempeiatuie foi theimostat (K)
atmsph taiget value foi the system piessuie (atm)
tautemp time constant foi Beienusen theimostat (psec)
taupies time constant foi Beienusen baiostat (psec)
compiess isotheimal compiessibility of meuium (atm-1)
colliue collision fiequency foi Anueisen theimostat
xnh position of each chaineu Nose-Boovei theimostat
vnh velocity of each chaineu Nose-Boovei theimostat
qnh mass foi each chaineu Nose-Boovei theimostat
gnh coupling between chaineu Nose-Boovei theimostats
isotheimal logical flag goveining use of tempeiatuie contiol
isobaiic logical flag goveining use of piessuie contiol
tempvaiy logical flag to enable vaiiable taiget theimostat
theimostat choice of tempeiatuie contiol methou to be useu
baiostat choice of piessuie contiol methou to be useu

V#"J' A/45+)/53) :/47/3 47* 6.++*34 )4+.64.+*

nbitoi total numbei of bitoisions in the system
ibitoi numbeis of the atoms in each bitoision

V$IGJ" )@*6/9/6) 59 A530 )4+*467 9.364/53;B 95+C)
142 "#$%&' ()*+,) -./0* 142

cbnu cubic coefficient in bonu stietch potential
qbnu quaitic coefficient in bonu stietch potential
bnuunit conveit bonu stietch eneigy to kcalmole
bnutyp type of bonu stietch potential eneigy function

VJ$I 65^;B*34 A530) /3 47* 6.++*34 )4+.64.+*

bk bonu stietch foice constants (kcalmoleAng**2)
bl iueal bonu length values in Angstioms
nbonu total numbei of bonu stietches in the system
ibnu numbeis of the atoms in each bonu stietch

VJ'I&' A530 5+0*+) 95+ ; 653j.X;4*0 @/)E)4*C

pbpl pi-bonu oiueis foi bonus in "planai" pisystem
pnpl pi-bonu oiueis foi bonus in "nonplanai" pisystem

VJ($I 6534+5B 59 @*+/50/6 A5.30;+E 6530/4/53)

polycut cutoff uistance foi infinite polymei nonbonus
polycut2 squaie of infinite polymei nonbonu cutoff
use_bounus flag to use peiiouic bounuaiy conuitions
use_image flag to use images foi peiiouic system
use_ieplica flag to use ieplicates foi peiiouic system
use_polymei flag to maik piesence of infinite polymei

VJQ&8 @;+;C*4*+) 95+ @*+/50/6 A5.30;+E 6530/4/53)

xbox length in Angs of a-axis of peiiouic box
ybox length in Angs of b-axis of peiiouic box
zbox length in Angs of c-axis of peiiouic box
alpha angle in uegiees between b- anu c-axes of box
beta angle in uegiees between a- anu c-axes of box
gamma angle in uegiees between a- anu b-axes of box
xbox2 half of the a-axis length of peiiouic box
ybox2 half of the b-axis length of peiiouic box
zbox2 half of the c-axis length of peiiouic box
boxS4 thiee-fouiths axis length of tiuncateu octaheuion
iecip iecipiocal lattice vectois as matiix columns
volbox volume in Ang**S of the peiiouic box
beta_sin sine of the beta peiiouic box angle
beta_cos cosine of the beta peiiouic box angle
gamma_sin sine of the gamma peiiouic box angle
gamma_cos cosine of the gamma peiiouic box angle
beta_teim teim useu in geneiating tiiclinic box
gamma_teim teim useu in geneiating tiiclinic box
oithogonal flag to maik peiiouic box as oithogonal
monoclinic flag to maik peiiouic box as monoclinic
tiiclinic flag to maik peiiouic box as tiiclinic
octaheuion flag to maik box as tiuncateu octaheuion
spacegip space gioup symbol foi the unitcell type
143 "#$%&' ()*+,) -./0* 143

?&PP @*+/50/6 A5.30;+/*) .)/3X +*@B/6;4*0 6*BB)

xcell length of the a-axis of the complete ieplicateu cell
ycell length of the b-axis of the complete ieplicateu cell
zcell length of the c-axis of the complete ieplicateu cell
xcell2 half the length of the a-axis of the ieplicateu cell
ycell2 half the length of the b-axis of the ieplicateu cell
zcell2 half the length of the c-axis of the ieplicateu cell
ncell total numbei of cell ieplicates foi peiiouic bounuaiies
icell offset along axes foi each ieplicate peiiouic cell

?YN'-& @;+4/;B 67;+X*) 95+ 47* 6.++*34 )4+.64.+*

pchg magnituue of the paitial chaiges (e-)
nion total numbei of paitial chaiges in system
iion numbei of the atom site foi each paitial chaige
jion neighboi geneiation site foi each paitial chaige
kion cutoff switching site foi each paitial chaige
chglist paitial chaige site foi each atom (u=no chaige)

?Y-GJ" )@*6/9/6) 59 67;+X*`67;+X* 9.364/53;B 95+C

uielec uielectiic constant foi electiostatic inteiactions
c2scale factoi by which 1-2 chaige inteiactions aie scaleu
cSscale factoi by which 1-S chaige inteiactions aie scaleu
c4scale factoi by which 1-4 chaige inteiactions aie scaleu
cSscale factoi by which 1-S chaige inteiactions aie scaleu
neutnbi logical flag goveining use of neutial gioup neighbois
neutcut logical flag goveining use of neutial gioup cutoffs

?Y'J$J 4/C/3X )4;4/)4/6) 95+ 47* 6.++*34 @+5X+;C

cputim elapseu cpu time in seconus since stait of piogiam

?J(GP& 3*;+`3*/X7A5+ ;45C 6533*64/^/4E B/)4)

maxn1S maximum numbei of atoms 1-S connecteu to an atom
maxn14 maximum numbei of atoms 1-4 connecteu to an atom
maxn1S maximum numbei of atoms 1-S connecteu to an atom
n12 numbei of atoms uiiectly bonueu to each atom
i12 atom numbeis of atoms 1-2 connecteu to each atom
n1S numbei of atoms in a 1-S ielation to each atom
i1S atom numbeis of atoms 1-S connecteu to each atom
n14 numbei of atoms in a 1-4 ielation to each atom
i14 atom numbeis of atoms 1-4 connecteu to each atom
n1S numbei of atoms in a 1-S ielation to each atom
i1S atom numbeis of atoms 1-S connecteu to each atom

?("J>> 6.4599 0/)4;36*) 95+ *3*+XE /34*+;64/53)

144 "#$%&' ()*+,) -./0* 144
vuwcut cutoff uistance foi van uei Waals inteiactions
chgcut cutoff uistance foi chaige-chaige inteiactions
uplcut cutoff uistance foi uipole-uipole inteiactions
mpolecut cutoff uistance foi atomic multipole inteiactions
vuwtapei uistance at which van uei Waals switching begins
chgtapei uistance at which chaige-chaige switching begins
upltapei uistance at which uipole-uipole switching begins
mpoletapei uistance at which atomic multipole switching begins
ewalucut cutoff uistance foi uiiect space Ewalu summation
use_ewalu logical flag goveining use of Ewalu summation teim
use_lights logical flag to use methou of lights neighbois

I&'#Z ?;+4*)/;3 655+0/3;4* 0*+/^;4/^* 65C@53*34)

uesum total eneigy Caitesian cooiuinate ueiivatives
ueb bonu stietch Caitesian cooiuinate ueiivatives
uea angle benu Caitesian cooiuinate ueiivatives
ueba stietch-benu Caitesian cooiuinate ueiivatives
ueub 0iey-Biauley Caitesian cooiuinate ueiivatives
ueaa angle-angle Caitesian cooiuinate ueiivatives
ueopb out-of-plane benu Caitesian cooiuinate ueiivatives
ueopu out-of-plane uistance Caitesian cooiuinate ueiivatives
ueiu impiopei uiheuial Caitesian cooiuinate ueiivatives
ueit impiopei toision Caitesian cooiuinate ueiivatives
uet toisional Caitesian cooiuinate ueiivatives
uept pi-oibital toision Caitesian cooiuinate ueiivatives
uebt stietch-toision Caitesian cooiuinate ueiivatives
uett toision-toision Caitesian cooiuinate ueiivatives
uev van uei Waals Caitesian cooiuinate ueiivatives
uec chaige-chaige Caitesian cooiuinate ueiivatives
uecu chaige-uipole Caitesian cooiuinate ueiivatives
ueu uipole-uipole Caitesian cooiuinate ueiivatives
uem multipole Caitesian cooiuinate ueiivatives
uep polaiization Caitesian cooiuinate ueiivatives
uei ieaction fielu Caitesian cooiuinate ueiivatives
ues solvation Caitesian cooiuinate ueiivatives
uelf metal liganu fielu Caitesian cooiuinate ueiivatives
ueg geometiic iestiaint Caitesian cooiuinate ueiivatives
uex extia eneigy teim Caitesian cooiuinate ueiivatives

I#GJP& ;45C M A530 0/@5B*) 95+ 6.++*34 )4+.64.+*

bupl magnituue of each of the uipoles (Bebyes)
supl position of each uipole between uefining atoms
nuipole total numbei of uipoles in the system
iupl numbeis of atoms that uefine each uipole

I#8-&J 0/)4;36* X*5C*4+E A5.30) ;30 @;+;C*4*+)

bnu uistance geometiy uppei anu lowei bounus matiix
vuwiau haiu spheie iauii foi uistance geometiy atoms
vuwmax maximum value of haiu spheie sum foi an atom paii
145 "#$%&' ()*+,) -./0* 145
compact inuex of local uistance compaction on embeuuing
pathmax maximum value of uppei bounu aftei smoothing
use_inveit flag to use enantiomei closest to input stiuctuie
use_anneal flag to use simulateu annealing iefinement

IJO&-N 0*+/^;4/^* 65C@53*34) 5^*+ 45+)/53)

tesum total eneigy ueiivatives ovei toisions
teb bonu stietch ueiivatives ovei toisions
tea angle benu ueiivatives ovei toisions
teba stietch-benu ueiivatives ovei toisions
teub 0iey-Biauley ueiivatives ovei toisions
teaa angle-angle ueiivatives ovei toisions
teopb out-of-plane benu ueiivatives ovei toisions
teopu out-of-plane uistance ueiivatives ovei toisions
teiu impiopei uiheuial ueiivatives ovei toisions
teit impiopei toision ueiivatives ovei toisions
tet toisional ueiivatives ovei toisions
tept pi-oibital toision ueiivatives ovei toisions
tebt stietch-toision ueiivatives ovei toisions
tett toision-toision ueiivatives ovei toisions
tev van uei Waals ueiivatives ovei toisions
tec chaige-chaige ueiivatives ovei toisions
tecu chaige-uipole ueiivatives ovei toisions
teu uipole-uipole ueiivatives ovei toisions
tem atomic multipole ueiivatives ovei toisions
tep polaiization ueiivatives ovei toisions
tei ieaction fielu ueiivatives ovei toisions
tes solvation ueiivatives ovei toisions
telf metal liganu fielu ueiivatives ovei toisions
teg geometiic iestiaint ueiivatives ovei toisions
tex extia eneigy teim ueiivatives ovei toisions

&$&'-# /30/^/0.;B @54*34/;B *3*+XE 65C@53*34)

esum total potential eneigy of the system
eb bonu stietch potential eneigy of the system
ea angle benu potential eneigy of the system
eba stietch-benu potential eneigy of the system
eub 0iey-Biauley potential eneigy of the system
eaa angle-angle potential eneigy of the system
eopb out-of-plane benu potential eneigy of the system
eopu out-of-plane uistance potential eneigy of the system
eiu impiopei uiheuial potential eneigy of the system
eit impiopei toision potential eneigy of the system
et toisional potential eneigy of the system
ept pi-oibital toision potential eneigy of the system
ebt stietch-toision potential eneigy of the system
ett toision-toision potential eneigy of the system
ev van uei Waals potential eneigy of the system
ec chaige-chaige potential eneigy of the system
ecu chaige-uipole potential eneigy of the system
eu uipole-uipole potential eneigy of the system
146 "#$%&' ()*+,) -./0* 146
em atomic multipole potential eneigy of the system
ep polaiization potential eneigy of the system
ei ieaction fielu potential eneigy of the system
es solvation potential eneigy of the system
elf metal liganu fielu potential eneigy of the system
eg geometiic iestiaint potential eneigy of the system
ex extia teim potential eneigy of the system

&<NPI @;+;C*4*+) 95+ +*X.B;+ 5+ GO &:;B0 ).CC;4/53

aewalu Ewalu conveigence coefficient value (Ang-1)
fiecip fiactional cutoff value foi iecipiocal spheie
tinfoil flag goveining use of tinfoil bounuaiy conuitions

&<'&- *H@53*34/;B 9;645+) 95+ +*X.B;+ &:;B0 ).C

maxvec maximum numbei of k-vectois pei iecipiocal axis
ejc exponental factois foi cosine along the j-axis
ejs exponental factois foi sine along the j-axis
ekc exponental factois foi cosine along the k-axis
eks exponental factois foi sine along the k-axis
elc exponental factois foi cosine along the l-axis
els exponental factois foi sine along the l-axis

>N?&8 ^;+/;AB*) 95+ ?5335BBE ;+*; ;30 ^5B.C*

maxnbi maximum numbei of neighboiing atom paiis
maxtt maximum numbei of tempoiaiy toii
maxt maximum numbei of total toii
maxp maximum numbei of piobe positions
maxv maximum numbei of veitices
maxen maximum numbei of concave euges
maxfn maximum numbei of concave faces
maxc maximum numbei of ciicles
maxep maximum numbei of convex euges
maxfs maximum numbei of sauule faces
maxcy maximum numbei of cycles
mxcyep maximum numbei of cycle convex euges
maxfp maximum numbei of convex faces
mxfpcy maximum numbei of convex face cycles

>#&PI8 C5B*6.B;+ C*67;3/6) 95+6* 9/*B0 0*)6+/@4/53

biotyp foice fielu atom type of each biopolymei type
foicefielu stiing useu to uesciibe the cuiient foicefielu

>#P&8 3;C* ;30 3.CA*+ 59 6.++*34 )4+.64.+* 9/B*)

npiioi numbei of pieviously existing cycle files
luii length in chaiacteis of the uiiectoiy name
leng length in chaiacteis of the base filename
147 "#$%&' ()*+,) -./0* 147
filename base filename useu by uefault foi all files
outfile output filename useu foi inteimeuiate iesults

>'N?8 ;45C 0/)4;36*) 45 C5B*6.B;+ 6*34*+ 59 C;))

xfiac fiactional cooiuinate along a-axis of centei of mass
yfiac fiactional cooiuinate along b-axis of centei of mass
zfiac fiactional cooiuinate along c-axis of centei of mass

-'J(G @;+4/4/53/3X 59 )E)4*C /345 ;45C X+5.@)

gipmass total mass of all the atoms in each gioup
wgip weight foi each set of gioup-gioup inteiactions
ngip total numbei of atom gioups in the system
kgip contiguous list of the atoms in each gioup
igip fiist anu last atom of each gioup in the list
giplist numbei of the gioup to which each atom belongs
use_gioup flag to use paititioning of system into gioups
use_intia flag to incluue only intiagioup inteiactions
use_intei flag to incluue only inteigioup inteiactions

Y&8?(" 6.4599 ^;B.* 95+ Y*))/;3 C;4+/H *B*C*34)

hesscut magnituue of smallest alloweu Bessian element

Y&88$ ?;+4*)/;3 Y*))/;3 *B*C*34) 95+ ; )/3XB* ;45C

hessx Bessian elements foi x-component of cuiient atom
hessy Bessian elements foi y-component of cuiient atom
hessz Bessian elements foi z-component of cuiient atom

#OG'JG /C@+5@*+ 0/7*0+;B) /3 47* 6.++*34 )4+.64.+*

kpiop foice constant values foi impiopei uiheuial angles
vpiop iueal impiopei uiheuial angle value in uegiees
nipiop total numbei of impiopei uiheuial angles in the system
iipiop numbeis of the atoms in each impiopei uiheuial angle

#OG"J' /C@+5@*+ 45+)/53) /3 47* 6.++*34 )4+.64.+*

itois1 1-folu amplituue anu phase foi each impiopei toision
itois2 2-folu amplituue anu phase foi each impiopei toision
itoisS S-folu amplituue anu phase foi each impiopei toision
nitois total numbei of impiopei toisional angles in the system
iitois numbeis of the atoms in each impiopei toisional angle

#$>J'O 6534+5B ^;B.*) 95+ #cJ ;30 @+5X+;C 9B5:

uigits uecimal places output foi eneigy anu cooiuinates
ipiint steps between status piinting (u=no piinting)
iwiite steps between cooiuinate uumps (u=no uumps)
148 "#$%&' ()*+,) -./0* 148
isenu steps between socket communication (u=no sockets)
veibose logical flag to tuin on extia infoimation
uebug logical flag to tuin on full uebug piinting
holuup logical flag to wait foi caiiiage ietuin on exit
aboit logical flag to stop execution at next chance

#$"&' ).C 59 /34*+C5B*6.B;+ *3*+XE 65C@53*34)

eintei total inteimoleculai potential eneigy

#J($#" >5+4+;3 /3@.4c5.4@.4 k#cJl .3/4 3.CA*+)

iout Foitian I0 unit foi majoi output (uefault=6)
input Foitian I0 unit foi majoi input (uefault=S)

%N$N$- 95+6*9/*B0 @;+;C*4*+) 95+ ;3XB*`;3XB* 4*+C)

anan angle-angle cioss teim paiameteis foi each atom class

%N$-8 95+6*9/*B0 @;+;C*4*+) 95+ A530 ;3XB* A*30/3X

maxna maximum numbei of haimonic angle benu paiametei entiies
maxnaS maximum numbei of S-membeieu iing angle benu entiies
maxna4 maximum numbei of 4-membeieu iing angle benu entiies
maxnaS maximum numbei of S-membeieu iing angle benu entiies
maxnaf maximum numbei of Fouiiei angle benu paiametei entiies
acon foice constant paiameteis foi haimonic angle benus
aconS foice constant paiameteis foi S-iing angle benus
acon4 foice constant paiameteis foi 4-iing angle benus
aconS foice constant paiameteis foi S-iing angle benus
aconf foice constant paiameteis foi Fouiiei angle benus
ang bonu angle paiameteis foi haimonic angle benus
angS bonu angle paiameteis foi S-iing angle benus
ang4 bonu angle paiameteis foi 4-iing angle benus
angS bonu angle paiameteis foi S-iing angle benus
angf phase shift angle anu peiiouicity foi Fouiiei benus
ka stiing of atom classes foi haimonic angle benus
kaS stiing of atom classes foi S-iing angle benus
ka4 stiing of atom classes foi 4-iing angle benus
kaS stiing of atom classes foi S-iing angle benus
kaf stiing of atom classes foi Fouiiei angle benus

%N"JO8 95+6*9/*B0 @;+;C*4*+) 95+ 47* ;45C 4E@*)

weight aveiage atomic mass of each atom type
atmcls atom class numbei foi each of the atom types
atmnum atomic numbei foi each of the atom types
liganu numbei of atoms to be attacheu to each atom type
symbol mouifieu atomic symbol foi each atom type
uesciibe stiing iuentifing each of the atom types

149 "#$%&' ()*+,) -./0* 149
%VJ$I8 95+6*9/*B0 @;+;C*4*+) 95+ A530 )4+*467/3X

maxnb maximum numbei of bonu stietch paiametei entiies
maxnbS maximum numbei of S-membeieu iing bonu stietch entiies
maxnb4 maximum numbei of 4-membeieu iing bonu stietch entiies
maxnbS maximum numbei of S-membeieu iing bonu stietch entiies
maxnel maximum numbei of electionegativity bonu coiiections
bcon foice constant paiameteis foi haimonic bonu stietch
bconS foice constant paiameteis foi S-iing bonu stietch
bcon4 foice constant paiameteis foi 4-iing bonu stietch
bconS foice constant paiameteis foi S-iing bonu stietch
blen bonu length paiameteis foi haimonic bonu stietch
blenS bonu length paiameteis foi S-iing bonu stietch
blen4 bonu length paiameteis foi 4-iing bonu stietch
blenS bonu length paiameteis foi S-iing bonu stietch
ulen electionegativity bonu length coiiection paiameteis
kb stiing of atom classes foi haimonic bonu stietch
kbS stiing of atom classes foi S-iing bonu stietch
kb4 stiing of atom classes foi 4-iing bonu stietch
kbS stiing of atom classes foi S-iing bonu stietch
kel stiing of atom classes foi electionegativity coiiections

%?Y'-& 95+6*9/*B0 @;+;C*4*+) 95+ @;+4/;B 67;+X*)

chg paitial chaige paiameteis foi each atom type

%I#GJP 95+6*9/*B0 @;+;C*4*+) 95+ A530 0/@5B*)

maxnu maximum numbei of bonu uipole paiametei entiies
maxnuS maximum numbei of S-membeieu iing uipole entiies
maxnu4 maximum numbei of 4-membeieu iing uipole entiies
maxnuS maximum numbei of S-membeieu iing uipole entiies
upl uipole moment paiameteis foi bonu uipoles
uplS uipole moment paiameteis foi S-iing uipoles
upl4 uipole moment paiameteis foi 4-iing uipoles
uplS uipole moment paiameteis foi S-iing uipoles
pos uipole position paiameteis foi bonu uipoles
posS uipole position paiameteis foi S-iing uipoles
pos4 uipole position paiameteis foi 4-iing uipoles
posS uipole position paiameteis foi S-iing uipoles
ku stiing of atom classes foi bonu uipoles
kuS stiing of atom classes foi S-iing uipoles
ku4 stiing of atom classes foi 4-iing uipoles
kuS stiing of atom classes foi S-iing uipoles

%&R8 6534*34) 59 6.++*34 m*E:5+0 @;+;C*4*+ 9/B*

nkey numbei of nonblank lines in the keywoiu file
keyline contents of each inuiviuual keywoiu file line

%-&JO8 @;+;C*4*+) 95+ 47* X*5C*4+/6;B +*)4+;/34)

150 "#$%&' ()*+,) -./0* 150
xpfix x-cooiuinate taiget foi each iestiaineu position
ypfix y-cooiuinate taiget foi each iestiaineu position
zpfix z-cooiuinate taiget foi each iestiaineu position
pfix foice constant anu flat-well iange foi each position
ufix foice constant anu taiget iange foi each uistance
afix foice constant anu taiget iange foi each angle
tfix foice constant anu taiget iange foi each toision
gfix foice constant anu taiget iange foi each gioup uistance
chii foice constant anu taiget iange foi chiial centeis
uepth uepth of shallow uaussian basin iestiaint
wiuth exponential wiuth coefficient of uaussian basin
iwall iauius of spheiical uioplet bounuaiy iestiaint
npfix numbei of position iestiaints to be applieu
ipfix atom numbei involveu in each position iestiaint
kpfix flags to use x-, y-, z-cooiuinate position iestiaints
nufix numbei of uistance iestiaints to be applieu
iufix atom numbeis uefining each uistance iestiaint
nafix numbei of angle iestiaints to be applieu
iafix atom numbeis uefining each angle iestiaint
ntfix numbei of toisional iestiaints to be applieu
itfix atom numbeis uefining each toisional iestiaint
ngfix numbei of gioup uistance iestiaints to be applieu
igfix gioup numbeis uefining each gioup uistance iestiaint
nchii numbei of chiiality iestiaints to be applieu
ichii atom numbeis uefining each chiiality iestiaint
use_basin logical flag goveining use of uaussian basin
use_wall logical flag goveining use of uioplet bounuaiy

%YVJ$I 95+6*9/*B0 @;+;C*4*+) 95+ Y`A530/3X 4*+C)

maxnhb maximum numbei of hyuiogen bonuing paii entiies
iauhb iauius paiametei foi hyuiogen bonuing paiis
epshb well uepth paiametei foi hyuiogen bonuing paiis
khb stiing of atom types foi hyuiogen bonuing paiis

%#G'JG 95+6*9/*B0 @;+;C*4*+) 95+ /C@+5@*+ 0/7*0+;B

maxnui maximum numbei of impiopei uiheuial paiametei entiies
ucon foice constant paiameteis foi impiopei uiheuials
tui iueal uiheuial angle values foi impiopei uiheuials
kui stiing of atom classes foi impiopei uiheuial angles

%#"J'8 95+6*9/*B0 @;+;C*4*+) 95+ /C@+5@*+ 45+)/53)

maxnti maximum numbei of impiopei toision paiametei entiies
ti1 toisional paiameteis foi impiopei 1-folu iotation
ti2 toisional paiameteis foi impiopei 2-folu iotation
tiS toisional paiameteis foi impiopei S-folu iotation
kti stiing of atom classes foi impiopei toisional paiameteis

%O(P"# 95+6*9/*B0 @;+;C*4*+) 95+ ;45C/6 C.B4/@5B*)

151 "#$%&' ()*+,) -./0* 151
maxnmp maximum numbei of atomic multipole paiametei entiies
multip atomic monopole, uipole anu quauiupole values
mpaxis type of local axis uefinition foi atomic multipoles
kmp stiing of atom types foi atomic multipoles

%JGV$I 95+6*9/*B0 @;+;C*4*+) 95+ 5.4`59`@B;3* A*30

maxnopb maximum numbei of out-of-plane benuing entiies
copb foice constant paiameteis foi out-of-plane benuing
kaopb stiing of atom classes foi out-of-plane benuing

%JGI8" 95+6*9/*B0 @;+;C*4*+) 95+ 5.4`@B;3* 0/)4;36*

maxnopb maximum numbei of out-of-plane uistance entiies
copb foice constant paiameteis foi out-of-plane uistance
kaopb stiing of atom classes foi out-of-plane uistance

%J'V8 95+6*9/*B0 @;+;C*4*+) 95+ @/)E)4*C 5+A/4;B)

maxnpi maximum numbei of pisystem bonu paiametei entiies
election numbei of pi-elections foi each atom class
ionize ionization potential foi each atom class
iepulse iepulsion integial value foi each atom class
sslope slope foi bonu stietch vs. pi-bonu oiuei
tslope slope foi 2-folu toision vs. pi-bonu oiuei
kpi stiing of atom classes foi pisystem bonus

%G#"J' 95+6*9/*B0 @;+;C*4*+) 95+ @/`5+A/4 45+)/53)

maxnpt maximum numbei of pi-oibital toision paiametei entiies
ptcon foice constant paiameteis foi pi-oibital toisions
kpt stiing of atom classes foi pi-oibital toision teims

%GJP' 95+6*9/*B0 @;+;C*4*+) 95+ @5B;+/\;A/B/4E

poli uipole polaiizability paiameteis foi each atom type
pgip connecteu types in polaiization gioup of each atom type

%8"V$I 95+6*9/*B0 @;+;C*4*+) 95+ )4+*467`A*30/3X

stbn stietch-benuing paiameteis foi each atom class

%8""J' 95+6*9/*B0 @;+;C*4*+) 95+ )4+*467`45+)/53)

maxnbt maximum numbei of stietch-toision paiametei entiies
btcon foice constant paiameteis foi stietch-toision
kbt stiing of atom classes foi bonus in stietch-toision

%"J'8$ 95+6*9/*B0 @;+;C*4*+) 95+ 45+)/53;B ;3XB*)

152 "#$%&' ()*+,) -./0* 152
maxnt maximum numbei of toisional angle paiametei entiies
maxntS maximum numbei of S-membeieu iing toision entiies
maxnt4 maximum numbei of 4-membeieu iing toision entiies
t1 toisional paiameteis foi stanuaiu 1-folu iotation
t2 toisional paiameteis foi stanuaiu 2-folu iotation
tS toisional paiameteis foi stanuaiu S-folu iotation
t4 toisional paiameteis foi stanuaiu 4-folu iotation
tS toisional paiameteis foi stanuaiu S-folu iotation
t6 toisional paiameteis foi stanuaiu 6-folu iotation
t1S toisional paiameteis foi 1-folu iotation in S-iing
t2S toisional paiameteis foi 2-folu iotation in S-iing
tSS toisional paiameteis foi S-folu iotation in S-iing
t4S toisional paiameteis foi 4-folu iotation in S-iing
tSS toisional paiameteis foi S-folu iotation in S-iing
t6S toisional paiameteis foi 6-folu iotation in S-iing
t14 toisional paiameteis foi 1-folu iotation in 4-iing
t24 toisional paiameteis foi 2-folu iotation in 4-iing
tS4 toisional paiameteis foi S-folu iotation in 4-iing
t44 toisional paiameteis foi 4-folu iotation in 4-iing
tS4 toisional paiameteis foi S-folu iotation in 4-iing
t64 toisional paiameteis foi 6-folu iotation in 4-iing
kt stiing of atom classes foi toisional angles
ktS stiing of atom classes foi S-iing toisions
kt4 stiing of atom classes foi 4-iing toisions

%"'"J' 95+6*9/*B0 @;+;C*4*+) 95+ 45+)/53`45+)/53)

maxntt maximum numbei of toision-toision paiametei entiies
maxtgiu maximum uimension of toision-toision spline giiu
maxtgiu2 maximum numbei of toision-toision spline giiu points
ttx angle values foi fiist toision of spline giiu
tty angle values foi seconu toision of spline giiu
tbf function values at points on spline giiu
tbx giauient ovei fiist toision of spline giiu
tby giauient ovei seconu toision of spline giiu
tbxy Bessian cioss components ovei spline giiu
tnx numbei of columns in toision-toision spline giiu
tny numbei of iows in toision-toision spline giiu
ktt stiing of toision-toision atom classes

%('RV' 95+6*9/*B0 @;+;C*4*+) 95+ (+*E`V+;0B*E 4*+C)

maxnu maximum numbei of 0iey-Biauley paiametei entiies
ucon foice constant paiameteis foi 0iey-Biauley teims
ust1S iueal 1-S uistance paiameteis foi 0iey-Biauley teims
ku stiing of atom classes foi 0iey-Biauley teims

%ZI<G' 95+6*9/*B0 @;+;C*4*+) 95+ )@*6/;B ^0:4*+C)

maxnvp maximum numbei of special van uei Waals paii entiies
iaupi iauius paiametei foi special van uei Waals paiis
epspi well uepth paiametei foi special van uei Waals paiis
153 "#$%&' ()*+,) -./0* 153
kvpi stiing of atom classes foi special van uei Waals paiis

%ZI<8 95+6*9/*B0 @;+;C*4*+) 95+ ^;3 0*+ <;;B) 4*+C)

iau van uei Waals iauius paiametei foi each atom class
eps van uei Waals well uepth paiametei foi each atom class
iau4 van uei Waals iauius paiametei in 1-4 inteiactions
eps4 van uei Waals well uepth paiametei in 1-4 inteiactions
ieuuct van uei Waals ieuuction factoi foi each atom class

P#-Y" /30/6*) 95+ C*4750 59 B/X74) @;/+ 3*/X7A5+)

nlight total numbei of sites foi methou of lights calculation
kbx low inuex of neighbois of each site in the x-soiteu list
kby low inuex of neighbois of each site in the y-soiteu list
kbz low inuex of neighbois of each site in the z-soiteu list
kex high inuex of neighbois of each site in the x-soiteu list
key high inuex of neighbois of each site in the y-soiteu list
kez high inuex of neighbois of each site in the z-soiteu list
locx pointei fiom x-soiteu list into oiiginal inteiaction list
locy pointei fiom y-soiteu list into oiiginal inteiaction list
locz pointei fiom z-soiteu list into oiiginal inteiaction list
igx pointei fiom oiiginal inteiaction list into x-soiteu list
igy pointei fiom oiiginal inteiaction list into y-soiteu list
igz pointei fiom oiiginal inteiaction list into z-soiteu list

P#$O#$ @;+;C*4*+) 95+ B/3* )*;+67 C/3/C/\;4/53

stpmin minimum step length in cuiient line seaich uiiection
stpmax maximum step length in cuiient line seaich uiiection
cappa stiingency of line seaich (u=tight < cappa < 1=loose)
slpmax piojecteu giauient above which stepsize is ieuuceu
angmax maximum angle between seaich uiiection anu -giauient
intmax maximum numbei of inteipolations uuiing line seaich

ON"Y C;47*C;4/6;B ;30 X*5C*4+/6;B 653)4;34)

iauian conveision factoi fiom iauians to uegiees
pi numeiical value of the geometiic constant
sqitpi numeiical value of the squaie ioot of Pi
logten numeiical value of the natuial log of ten
sqittwo numeiical value of the squaie ioot of two
twosix numeiical value of the sixth ioot of two

OI8"(> 6534+5B 59 C5B*6.B;+ 0E3;C/6) 4+;j*645+E

nfiee total numbei of uegiees of fieeuom foi a system
velsave flag to save velocity vectoi components to a file
ficsave flag to save foice vectoi components to a file
uinusave flag to save inuuceu atomic uipoles to a file
integiate type of moleculai uynamics integiation algoiithm
154 "#$%&' ()*+,) -./0* 154

O#$#ON X*3*+;B @;+;C*4*+) 95+ C/3/C/\;4/53)

fctmin value below which function is ueemeu optimizeu
hguess initial value foi the B-matiix uiagonal elements
maxitei maximum numbei of iteiations uuiing optimization
nextitei iteiation numbei to use foi the fiist iteiation

OJP?(P /30/^/0.;B C5B*6.B*) :/47/3 6.++*34 )E)4*C

molmass moleculai weight foi each molecule in the system
totmass total weight of all the molecules in the system
nmol total numbei of sepaiate molecules in the system
kmol contiguous list of the atoms in each molecule
imol fiist anu last atom of each molecule in the list
molcule numbei of the molecule to which each atom belongs

OJPIR$ ^*B56/4E ;30 ;66*B*+;4/53 53 OI 4+;j*645+E

v cuiient velocity of each atom along the x,y,z-axes
a cuiient acceleiation of each atom along x,y,z-axes
aolu pievious acceleiation of each atom along x,y,z-axes

OJO&$" 65C@53*34) 59 *B*64+/6 C.B4/@5B* C5C*34)

netchg net electiic chaige foi the total system
netupl uipole moment magnituue foi the total system
netqup uiagonal quauiupole (Qxx, Qyy, Qzz) foi system
xupl uipole vectoi x-component in the global fiame
yupl uipole vectoi y-component in the global fiame
zupl uipole vectoi z-component in the global fiame
xxqup quauiupole tensoi xx-component in global fiame
xyqup quauiupole tensoi xy-component in global fiame
xzqup quauiupole tensoi xz-component in global fiame
yxqup quauiupole tensoi yx-component in global fiame
yyqup quauiupole tensoi yy-component in global fiame
yzqup quauiupole tensoi yz-component in global fiame
zxqup quauiupole tensoi zx-component in global fiame
zyqup quauiupole tensoi zy-component in global fiame
zzqup quauiupole tensoi zz-component in global fiame

OGPGJ" )@*6/9/6) 59 ;45C/6 C.B4/@5B* 9.364/53)

m2scale factoi by which 1-2 multipole inteiactions aie scaleu
mSscale factoi by which 1-S multipole inteiactions aie scaleu
m4scale factoi by which 1-4 multipole inteiactions aie scaleu
mSscale factoi by which 1-S multipole inteiactions aie scaleu

OGJP& C.B4/@5B* 65C@53*34) 95+ 6.++*34 )4+.64.+*

maxpole max components (monopole=1,uipole=4,quauiupole=1S)
155 "#$%&' ()*+,) -./0* 155
pole multipole values foi each site in the local fiame
ipole multipoles iotateu to the global cooiuinate system
npole total numbei of multipole sites in the system
ipole numbei of the atom foi each multipole site
polsiz numbei of mutipole components at each multipole site
zaxis numbei of the z-axis uefining atom foi each site
xaxis numbei of the x-axis uefining atom foi each site
yaxis numbei of the y-axis uefining atom foi each site
polaxe local axis type foi each multipole site

O("N$" 7EA+/0 ;45C) 95+ 9+** *3*+XE @*+4.+A;4/53

lambua weighting of initial state in hybiiu Bamiltonian
nhybiiu numbei of atoms mutateu fiom initial to final state
ihybiiu atomic sites uiffeiing in initial anu final state
typeu atom type of each atom in the initial state system
classu atom class of each atom in the initial state system
type1 atom type of each atom in the final state system
class1 atom class of each atom in the final state system
altei tiue if an atom is to be mutateu, false otheiwise

$(?P&J @;+;C*4*+) 95+ 3.6B*/6 ;6/0 )4+.64.+*

bkbone phosphate backbone angles foi each nucleotiue
glyco glycosiuic toisional angle foi each nucleotiue
puckei sugai puckei, eithei 2=2'-enuo oi S=S'-enuo
ublhlx flag to maik system as nucleic aciu uouble helix
ueoxy flag to maik ueoxyiibose oi iibose sugai units
hlxfoim helix foim (A, B oi Z) of polynucleotiue stianus

JO&-N 0/7*0+;B) 95+ 45+)/53;B )@;6* 65C@.4;4/53)

uiheu cuiient value in iauians of each uiheuial angle
nomega numbei of uiheuial angles alloweu to iotate
iomega numbeis of two atoms uefining iotation axis
zline line numbei in Z-matiix of each uiheuial angle

JGV&$I 5.4`59`@B;3* A*30) /3 47* 6.++*34 )4+.64.+*

kopb foice constant values foi out-of-plane benuing
nopbenu total numbei of out-of-plane benus in the system
iopb bonu angle numbeis useu in out-of-plane benuing

JGI#8" 5.4`59`@B;3* 0/)4;36*) /3 6.++*34 )4+.64.+*

kopu foice constant values foi out-of-plane uistance
nopuist total numbei of out-of-plane uistances in the system
iopb numbeis of the atoms in each out-of-plane uistance

J'V#"8 5+A/4;B *3*+X/*) 95+ 653j.X;4*0 @/)E)4*C

156 "#$%&' ()*+,) -./0* 156
q numbei of pi-elections contiibuteu by each atom
w ionization potential of each pisystem atom
em iepulsion integial foi each pisystem atom
nfill numbei of filleu pisystem moleculai oibitals

J("G(" 6534+5B 59 655+0/3;4* 5.4@.4 9/B* 95+C;4

aichive logical flag to save stiuctuies in an aichive
noveision logical flag goveining use of filename veisions
oveiwiite logical flag to oveiwiite inteimeuiate files inplace
cyclesave logical flag to maik use of numbeieu cycle files
cooiutype selects Caitesian, inteinal, iigiu bouy oi none

GN'NO8 6534*34) 59 95+6* 9/*B0 @;+;C*4*+ 9/B*

npim numbei of nonblank lines in the paiametei file
pimline contents of each inuiviuual paiametei file line

GN"Y8 @;+;C*4*+) 95+ &BA*+ +*;64/53 @;47 C*4750

pu ieactant Caitesian cooiuinates as vaiiables
p1 piouuct Caitesian cooiuinates as vaiiables
pmiu miupoint between the ieactant anu piouuct
pvect vectoi connecting the ieactant anu piouuct
pstep step pei cycle along ieactant-piouuct vectoi
pzet cuiient piojection on ieactant-piouuct vectoi
pnoim length of the ieactant-piouuct vectoi
acoeff tiansfoimation matiix 'A' fiom Elbei papei
gc giauients of the path constiaints

GIV 0*9/3/4/53 59 ; G+54*/3 I;4; V;3m )4+.64.+*

xpub x-cooiuinate of each atom stoieu in PBB foimat
ypub y-cooiuinate of each atom stoieu in PBB foimat
zpub z-cooiuinate of each atom stoieu in PBB foimat
npub numbei of atoms stoieu in Piotein Bata Bank foimat
iesnum numbei of the iesiuue to which each atom belongs
npub12 numbei of atoms uiiectly bonueu to each C0NECT atom
ipub12 atom numbeis of atoms connecteu to each C0NECT atom
publist list of the Piotein Bata Bank atom numbei of each atom
pubtyp Piotein Bata Bank iecoiu type assigneu to each atom
atmnam Piotein Bata Bank atom name assigneu to each atom
iesnam Piotein Bata Bank iesiuue name assigneu to each atom

GY#G8# @7/`@)/`5C*X;`67/ ;3XB*) 95+ ; @+54*/3

phi value of the phi angle foi each amino aciu iesiuue
psi value of the psi angle foi each amino aciu iesiuue
omega value of the omega angle foi each amino aciu iesiuue
chi values of the chi angles foi each amino aciu iesiuue
chiial chiiality of each amino aciu iesiuue (1=L, -1=B)
157 "#$%&' ()*+,) -./0* 157
uisulf iesiuue joineu to each iesiuue via a uisulfiue link

G#J'V8 653j.X;4*0 )E)4*C /3 47* 6.++*34 )4+.64.+*

noibit total numbei of pisystem oibitals in the system
ioibit numbeis of the atoms containing pisystem oibitals
ieoibit numbei of evaluations between oibital upuates
pipeip atoms uefining a noimal plane to each oibital
nbpi total numbei of bonus affecteu by the pisystem
bpi bonu anu piatom numbeis foi each pisystem bonu
ntpi total numbei of toisions affecteu by the pisystem
tpi toision anu pibonu numbeis foi each pisystem toision
listpi atom list inuicating whethei each atom has an oibital

G#8"(> A530) ;30 45+)/53) /3 47* 6.++*34 @/)E)4*C

bkpi bonu stietch foice constants foi pi-bonu oiuei of 1.u
blpi iueal bonu length values foi a pi-bonu oiuei of 1.u
kslope iate of foice constant ueciease with bonu oiuei ueciease
lslope iate of bonu length inciease with a bonu oiuei ueciease
toisp2 2-folu toisional eneigy baiiiei foi pi-bonu oiuei of 1.u

G#"J'8 @/`5+A/4;B 45+)/53) /3 47* 6.++*34 )4+.64.+*

kpit 2-folu pi-oibital toisional foice constants
npitois total numbei of pi-oibital toisional inteiactions
ipit numbeis of the atoms in each pi-oibital toision

GO& @;+;C*4*+) 95+ @;+4/6B* C*)7 &:;B0 ).CC;4/53

maxfft maximum numbei of points along each FFT uiiection
maxoiuei maximum oiuei of the B-spline appioximation
maxtable maximum size of the FFT table aiiay
maxgiiu maximum uimension of the PNE chaige giiu aiiay
bsmou1 B-spline mouuli along the a-axis uiiection
bsmou2 B-spline mouuli along the b-axis uiiection
bsmouS B-spline mouuli along the c-axis uiiection
table inteimeuiate aiiay useu by the FFT calculation
nfft1 numbei of giiu points along the a-axis uiiection
nfft2 numbei of giiu points along the b-axis uiiection
nfftS numbei of giiu points along the c-axis uiiection
bsoiuei oiuei of the PNE B-spline appioximation

GJPN' @5B;+/\;A/B/4/*) ;30 /30.6*0 0/@5B* C5C*34)

polaiity uipole polaiizability foi each multipole site (Ang**S)
puamp value of polaiizability uamping factoi foi each site
uinu inuuceu uipole components at each multipole site
uinp inuuceu uipoles in fielu useu foi eneigy inteiactions
npolai total numbei of polaiizable sites in the system

158 "#$%&' ()*+,) -./0* 158
GJP-'G @5B;+/\;AB* )/4* X+5.@ 6533*64/^/4E B/)4)

maxp11 maximum numbei of atoms in a polaiization gioup
maxp12 maximum numbei of atoms in gioups 1-2 to an atom
maxp1S maximum numbei of atoms in gioups 1-S to an atom
maxp14 maximum numbei of atoms in gioups 1-4 to an atom
np11 numbei of atoms in polaiization gioup of each atom
ip11 atom numbeis of atoms in same gioup as each atom
np12 numbei of atoms in gioups 1-2 to each atom
ip12 atom numbeis of atoms in gioups 1-2 to each atom
np1S numbei of atoms in gioups 1-S to each atom
ip1S atom numbeis of atoms in gioups 1-S to each atom
np14 numbei of atoms in gioups 1-4 to each atom
ip14 atom numbeis of atoms in gioups 1-4 to each atom

GJPGJ" )@*6/9/6) 59 @5B;+/\;4/53 9.364/53;B 95+C

poleps inuuceu uipole conveigence ciiteiion (ims Bebyesatom)
polsoi inuuceu uipole S0R conveigence acceleiation factoi
pgamma piefactoi in exponential polaiization uamping teim
p2scale fielu 1-2 scale factoi foi eneigy evaluations
pSscale fielu 1-S scale factoi foi eneigy evaluations
p4scale fielu 1-4 scale factoi foi eneigy evaluations
pSscale fielu 1-S scale factoi foi eneigy evaluations
u1scale fielu intia-gioup scale factoi foi uiiect inuuceu
u2scale fielu 1-2 gioup scale factoi foi uiiect inuuceu
uSscale fielu 1-S gioup scale factoi foi uiiect inuuceu
u4scale fielu 1-4 gioup scale factoi foi uiiect inuuceu
u1scale fielu intia-gioup scale factoi foi mutual inuuceu
u2scale fielu 1-2 gioup scale factoi foi mutual inuuceu
uSscale fielu 1-S gioup scale factoi foi mutual inuuceu
u4scale fielu 1-4 gioup scale factoi foi mutual inuuceu
poltyp type of polaiization potential (uiiect oi mutual)

GJ"&$" .);X* 59 *;67 @54*34/;B *3*+XE 65C@53*34

use_bonu logical flag goveining use of bonu stietch potential
use_angle logical flag goveining use of angle benu potential
use_stibnu logical flag goveining use of stietch-benu potential
use_uiey logical flag goveining use of 0iey-Biauley potential
use_angang logical flag goveining use of angle-angle cioss teim
use_opbenu logical flag goveining use of out-of-plane benu teim
use_opuist logical flag goveining use of out-of-plane uistance
use_impiop logical flag goveining use of impiopei uiheuial teim
use_imptoi logical flag goveining use of impiopei toision teim
use_tois logical flag goveining use of toisional potential
use_pitois logical flag goveining use of pi-oibital toision teim
use_stitoi logical flag goveining use of stietch-toision teim
use_toitoi logical flag goveining use of toision-toision teim
use_vuw logical flag goveining use of vuw uei Waals potential
use_chaige logical flag goveining use of chaige-chaige potential
use_chgupl logical flag goveining use of chaige-uipole potential
159 "#$%&' ()*+,) -./0* 159
use_uipole logical flag goveining use of uipole-uipole potential
use_mpole logical flag goveining use of multipole potential
use_polai logical flag goveining use of polaiization teim
use_ixnflu logical flag goveining use of ieaction fielu teim
use_solv logical flag goveining use of suiface aiea solvation
use_gbsa logical flag goveining use of uBSA solvation teim
use_metal logical flag goveining use of liganu fielu teim
use_geom logical flag goveining use of geometiic iestiaints
use_extia logical flag goveining use of extia potential teim
use_oibit logical flag goveining use of pisystem computation

G'&?#8 ^;B.*) 59 C;67/3* @+*6/)/53 45B*+;36*)

tiny the smallest positive floating point value
small the smallest ielative floating point spacing
huge the laigest ielative floating point spacing

'&>&' )45+;X* 59 +*9*+*36* ;45C/6 655+0/3;4* )*4

xief iefeience x-cooiuinate foi each atom in the system
yief iefeience y-cooiuinate foi each atom in the system
zief iefeience z-cooiuinate foi each atom in the system
nief total numbei of atoms in the iefeience system
ieftyp atom type foi each atom in the iefeience system
n12ief numbei of atoms bonueu to each iefeience atom
i12ief atom numbeis of atoms 1-2 connecteu to each atom
iefleng length in chaiacteis of the iefeience filename
iefltitle length in chaiacteis of the iefeience title stiing
iefnam atom name foi each atom in the iefeience system
ieffile base filename foi the iefeience stiuctuie
ieftitle title useu to uesciibe the iefeience stiuctuie

'&8I(& )4;30;+0 A/5@5BEC*+ +*)/0.* ;AA+*^/;4/53)

amino thiee-lettei abbieviations foi amino acius types
nuclz thiee-lettei abbieviations foi nucleic acius types
amino1 one-lettei abbieviations foi amino acius types
nuclz1 one-lettei abbieviations foi nucleic acius types

'-IIR$ ^*B56/4/*) ;30 C5C*34; 95+ +/X/0 A50E OI

vcm cuiient tianslational velocity of each iigiu bouy
wcm cuiient angulai velocity of each iigiu bouy
lm cuiient angulai momentum of each iigiu bouy
lineai logical flag to maik gioup as lineai oi nonlineai

'#-#I +/X/0 A50E 655+0/3;4*) 95+ ;45C X+5.@)

xib iigiu bouy iefeience x-cooiuinate foi each atom
yib iigiu bouy iefeience y-cooiuinate foi each atom
zib iigiu bouy iefeience z-cooiuinate foi each atom
160 "#$%&' ()*+,) -./0* 160
ibc cuiient iigiu bouy cooiuinates foi each gioup
use_iigiu flag to maik use of iigiu bouy cooiuinate system

'#$- 3.CA*+ ;30 B56;4/53 59 )C;BB +/3X )4+.64.+*)

niingS total numbei of S-membeieu iings in the system
iiingS numbeis of the atoms involveu in each S-iing
niing4 total numbei of 4-membeieu iings in the system
iiing4 numbeis of the atoms involveu in each 4-iing
niingS total numbei of S-membeieu iings in the system
iiingS numbeis of the atoms involveu in each S-iing
niing6 total numbei of 6-membeieu iings in the system
iiing6 numbeis of the atoms involveu in each 6-iing

'J"N"& C5B*6.B* @;+4/4/53) 95+ +54;4/53 59 ; A530

niot total numbei of atoms moving when bonu iotates
iot atom numbeis of atoms moving when bonu iotates
use_shoit logical flag goveining use of shoitest atom list

'Q$>PI +*;64/53 9/*B0 C;4+/H *B*C*34) ;30 /30/6*)

b1 fiist ieaction fielu matiix element aiiay
b2 seconu ieaction fielu matiix element aiiay
ijk inuices into the ieaction fielu element aiiays

'Q$GJ" )@*6/9/6) 59 +*;64/53 9/*B0 9.364/53;B 95+C

ifsize iauius of ieaction fielu spheie centeieu at oiigin
ifbulku bulk uielectiic constant of ieaction fielu continuum
ifteims numbei of teims to use in ieaction fielu summation

8?NP&8 @;+;C*4*+ )6;B* 9;645+) 95+ 5@4/C/\;4/53

scale multiplicative factoi foi each optimization paiametei
set_scale logical flag to show if scale factois have been set

8&K(&$ )*d.*36* /395+C;4/53 95+ ; A/5@5BEC*+

nseq total numbei of iesiuues in biopolymei sequences
nchain numbei of sepaiate biopolymei sequence chains
ichain fiist anu last iesiuue in each biopolymei chain
seqtyp iesiuue type foi each iesiuue in the sequence
seq thiee-lettei coue foi each iesiuue in the sequence
chnnam one-lettei iuentifiei foi each sequence chain

8YN%& 0*9/3/4/53 59 87;m*c';44B* 653)4+;/34)

kiat iueal uistance value foi iattle constiaint
niat numbei of iattle uistance constiaints to apply
niatx numbei of atom gioup spatial constiaints to apply
161 "#$%&' ()*+,) -./0* 161
iiat atom numbeis of atoms in a iattle constiaint
iiatx gioup numbei of gioup in a spatial constiaint
kiatx spatial constiaint type (1=plane, 2=line, S=point)
iatimage flag to use minimum image foi iattle constiaint
use_iattle logical flag to set use of iattle contiaints

8Y($" @5BE35C/;B ):/467/3X 9.364/53 65*99/6/*34)

off uistance at which the potential eneigy goes to zeio
off2 squaie of uistance at which the potential goes to zeio
cut uistance at which switching of the potential begins
cut2 squaie of uistance at which the switching begins
cu zeioth oiuei coefficient of multiplicative switch
c1 fiist oiuei coefficient of multiplicative switch
c2 seconu oiuei coefficient of multiplicative switch
cS thiiu oiuei coefficient of multiplicative switch
c4 fouith oiuei coefficient of multiplicative switch
cS fifth oiuei coefficient of multiplicative switch
fu zeioth oiuei coefficient of auuitive switch function
f1 fiist oiuei coefficient of auuitive switch function
f2 seconu oiuei coefficient of auuitive switch function
fS thiiu oiuei coefficient of auuitive switch function
f4 fouith oiuei coefficient of auuitive switch function
fS fifth oiuei coefficient of auuitive switch function
f6 sixth oiuei coefficient of auuitive switch function
f7 seventh oiuei coefficient of auuitive switch function

8#S&8 @;+;C*4*+ ^;B.*) 45 )*4 ;++;E 0/C*3)/53)

"sizes.i" sets values foi ciitical aiiay uimensions useu thioughout the softwaie; these paiameteis will
fix the size of the laigest systems that can be hanuleu; values too laige foi the computei's memoiy
anuoi swap space to accomouate will iesult in pooi peifoimance oi outiight failuie

paiametei: maximum alloweu numbei of:

maxatm atoms in the moleculai system
maxval atoms uiiectly bonueu to an atom
maxgip usei-uefineu gioups of atoms
maxtyp foice fielu atom type uefinitions
maxclass foice fielu atom class uefinitions
maxpim lines in the paiametei file
maxkey lines in the keywoiu file
maxiot bonus foi toisional iotation
maxvai optimization vaiiables (vectoi stoiage)
maxopt optimization vaiiables (matiix stoiage)
maxhess off-uiagonal Bessian elements
maxlight sites foi methou of lights neighbois
maxvib vibiational fiequencies
maxgeo uistance geometiy points
maxcell unit cells in ieplicateu ciystal
maxiing S-, 4-, oi S-membeieu iings
maxfix geometiic constiaints anu iestiaints
162 "#$%&' ()*+,) -./0* 162
maxbio biopolymei atom uefinitions
maxies iesiuues in the maciomolecule
maxamino amino aciu iesiuue types
maxnuc nucleic aciu iesiuue types
maxbnu covalent bonus in moleculai system
maxang bonu angles in moleculai system
maxtois toisional angles in moleculai system
maxbitoi bitoisions in moleculai system
maxpi atoms in conjugateu pisystem
maxpib covalent bonus involving pisystem
maxpit toisional angles involving pisystem

8J?%&" 6534+5B @;+;C*4*+) 95+ )56m*4 65CC.3/6;4/53

iuntyp calculation type foi passing socket infoimation
cstep cuiient optimization oi uynamics step numbei
cut cuiient uynamics cumulative simulation time
ceneigy cuiient potential eneigy fiom simulation
cux cuiient giauient components along the x-axis
cuy cuiient giauient components along the y-axis
cuz cuiient giauient components along the z-axis
skt_init logical flag set to tiue aftei socket initialization
use_socket logical flag goveining use of exteinal sockets
use_gui logical flag to show TINKER was invokeu fiom u0I
closing logical flag to inuicate }vN anu seivei shutuown

8JP("& @;+;C*4*+) 95+ 6534/3..C )5B^;4/53 C50*B)

isolv atomic iauius of each atom foi continuum solvation
vsolv atomic volume of each atom foi continuum solvation
asolv atomic solvation paiameteis (kcalmoleAng**2)
iboin Boin iauius of each atom foi uBSA solvation
uib solvation ueiivatives with iespect to Boin iauii
uoffset uielectiic offset to continuum solvation atomic iauii
p1 single-atom scale factoi foi analytical Still uBSA
p2 1-2 inteiaction scale factoi foi analytical Still uBSA
pS 1-S inteiaction scale factoi foi analytical Still uBSA
p4 nonbonueu scale factoi foi analytical Still uBSA
pS soft cutoff paiametei foi analytical Still uBSA
gpol polaiization self-eneigy values foi each atom
shct oveilap scaling factois foi Bawkins-Ciamei-Tiuhlai uBSA
wace "omega" values foi atom class paiis foi use with ACE
s2ace "sigma^2" values foi atom class paiis foi use with ACE
uace "mu" values foi atom class paiis foi use with ACE
solvtyp solvation mouel (ASP, SASA, 0NI0N, STILL, BCT, ACE)

8"JIR$ 9+/64/53;B 65*99/6/*34) 95+ 8I 4+;j*645+E

fiiction global fiictional coefficient foi exposeu paiticle
gamma atomic fiictional coefficients foi each atom
use_suaiea logical flag to use suiface aiea fiiction scaling

163 "#$%&' ()*+,) -./0* 163
8"'V$I )4+*467`A*30) /3 47* 6.++*34 )4+.64.+*

ksb foice constant foi stietch-benu teims
nstibnu total numbei of stietch-benu inteiactions
isb angle anu bonu numbeis useu in stietch-benu

8"'"J' )4+*467`45+)/53) /3 47* 6.++*34 )4+.64.+*

kst 1-, 2- anu S-folu stietch-toision foice constants
nstitoi total numbei of stietch-toision inteiactions
ist toision anu bonu numbeis useu in stietch-toision

8R$"'$ 0*9/3/4/53 59 )E367+535.) 4+;3)/4 @;47

t value of the path cooiuinate (u=ieactant, 1=piouuct)
pm path cooiuinate foi extia point in quauiatic tiansit
xmin1 ieactant cooiuinates as aiiay of optimization vaiiables
xmin2 piouuct cooiuinates as aiiay of optimization vaiiables
xm extia cooiuinate set foi quauiatic synchionous tiansit

"#"P&8 4/4B* 95+ 47* 6.++*34 C5B*6.B;+ )E)4*C

ltitle length in chaiacteis of the nonblank title stiing
title title useu to uesciibe the cuiient stiuctuie

"J'GJ" )@*6/9/6) 59 45+)/53;B 9.364/53;B 95+C)

iuihunit conveit impiopei uiheuial eneigy to kcalmole
itoiunit conveit impiopei toision amplituues to kcalmole
toisunit conveit toisional paiametei amplituues to kcalmole
ptoiunit conveit pi-oibital toision eneigy to kcalmole
stoiunit conveit stietch-toision eneigy to kcalmole
ttoiunit conveit stietch-toision eneigy to kcalmole

"J'8 45+)/53;B ;3XB*) :/47/3 47* 6.++*34 )4+.64.+*

tois1 1-folu amplituue anu phase foi each toisional angle
tois2 2-folu amplituue anu phase foi each toisional angle
toisS S-folu amplituue anu phase foi each toisional angle
tois4 4-folu amplituue anu phase foi each toisional angle
toisS S-folu amplituue anu phase foi each toisional angle
tois6 6-folu amplituue anu phase foi each toisional angle
ntois total numbei of toisional angles in the system
itois numbeis of the atoms in each toisional angle

"J'"J' 45+)/53`45+)/53) /3 47* 6.++*34 )4+.64.+*

ntoitoi total numbei of toision-toision inteiactions
itt atoms anu paiametei inuices foi toision-toision

"'&& @54*34/;B )C5547/3X M )*;+67 4+** B*^*B)
164 "#$%&' ()*+,) -./0* 164

maxpss maximum numbei of potential smoothing levels
etiee eneigy iefeience value at the top of the tiee
ilevel smoothing uefoimation value at each tiee level
nlevel numbei of levels of potential smoothing useu

($#"8 @7E)/6;B 653)4;34) ;30 .3/4 653^*+)/53)

avogauio Avogauio's numbei (N) in paiticlesmole
boltzmann Boltzmann constant (kB) in g*Ang**2ps**2Kmole
gasconst iueal gas constant (R) in kcalmoleK
lightspu speeu of light in vacuum (c) in cmps
bohi conveision fiom Bohis to Angstioms
joule conveision fiom caloiies to joules
evolt conveision fiom Baitiee to election-volts
haitiee conveision fiom Baitiee to kcalmole
electiic conveision fiom election**2Ang to kcalmole
uebye conveision fiom election-Ang to Bebyes
piescon conveision fiom kcalmoleAng**S to Atm
conveit conveision fiom kcal to g*Ang**2ps**2

('&R (+*E`V+;0B*E /34*+;64/53) /3 47* )4+.64.+*

uk 0iey-Biauley foice constants (kcalmoleAng**2)
ul iueal 1-S uistance values in Angstioms
nuiey total numbei of 0iey-Biauley teims in the system
iuiy numbeis of the atoms in each 0iey-Biauley inteiaction

('RGJ" )@*6/9/6) 59 (+*E`V+;0B*E 9.364/53;B 95+C

cuiy cubic coefficient in 0iey-Biauley potential
quiy quaitic coefficient in 0iey-Biauley potential
uieyunit conveit 0iey-Biauley eneigy to kcalmole

(8N-& ;45C) ;64/^* 0.+/3X *3*+XE 65C@.4;4/53

nuse numbei of active atoms useu in eneigy calculation
use tiue if an atom is active, false if inactive

ZI< ^;3 0*+ <;;B) @;+;C*4*+) 95+ 6.++*34 )4+.64.+*

iaumin minimum eneigy uistance foi each atom class paii
epsilon well uepth paiametei foi each atom class paii
iaumin4 minimum eneigy uistance foi 1-4 inteiaction paiis
epsilon4 well uepth paiametei foi 1-4 inteiaction paiis
iauhbnu minimum eneigy uistance foi hyuiogen bonuing paiis
epshbnu well uepth paiametei foi hyuiogen bonuing paiis
kieu value of ieuuction factoi paiametei foi each atom
iieu attacheu atom fiom which ieuuction factoi is applieu
nvuw total numbei van uei Waals active sites in the system
ivuw numbei of the atom foi each van uei Waals active site
165 "#$%&' ()*+,) -./0* 165

ZI<GJ" )@*6/9/6) 59 ^;3 0*+ <;;B) 9.364/53;B 95+C

abuck value of "A" constant in Buckingham vuw potential
bbuck value of "B" constant in Buckingham vuw potential
cbuck value of "C" constant in Buckingham vuw potential
ghal value of "gamma" in buffeieu 14-7 vuw potential
uhal value of "uelta" in buffeieu 14-7 vuw potential
v2scale factoi by which 1-2 vuw inteiactions aie scaleu
vSscale factoi by which 1-S vuw inteiactions aie scaleu
v4scale factoi by which 1-4 vuw inteiactions aie scaleu
vSscale factoi by which 1-S vuw inteiactions aie scaleu
igauss coefficients of uaussian fit to vuw potential
ngauss numbei of uaussians useu in fit to vuw potential
vuwtyp type of van uei Waals potential eneigy function
iautyp type of paiametei (sigma oi R-min) foi atomic size
iausiz atomic size pioviueu as iauius oi uiametei
iauiule combining iule foi atomic size paiameteis
epsiule combining iule foi vuw well uepth paiameteis
gausstyp type of uaussian fit to van uei Waals potential

Z#'#NP 65C@53*34) 59 /34*+3;B ^/+/;B 4*3)5+

vii total inteinal viiial Caitesian tensoi components

<N'G @;+;C*4*+) 95+ @54*34/;B ).+9;6* )C5547/3X

m2 seconu moment of the uBA gaussian foi each atom
uefoim value of the smoothing uefoimation paiametei
uifft uiffusion coefficient foi toisional potential
uiffv uiffusion coefficient foi van uei Waals potential
uiffc uiffusion coefficient foi chaige-chaige potential
use_smooth flag to use a potential eneigy smoothing methou
use_uem flag to use uiffusion equation methou potential
use_gua flag to use gaussian uensity annealing potential
use_tophat flag to use analytical tophat smootheu potential
use_stophat flag to use shifteu tophat smootheu potential

Q"NP8 6+E)4;B )4+.64.+*) 95+ @;+;C*4*+ 9/44/3X

eu_lattice iueal lattice eneigy foi the cuiient ciystal
moment_u iueal uipole moment foi monomei fiom ciystal
nxtal numbei of ciystal stiuctuies to be stoieu
nvaiy numbei of potential paiameteis to optimize
ivaiy inuex foi the types of potential paiameteis
vaiy atom numbeis involveu in potential paiameteis
iiesiu ciystal stiuctuie to which each iesiuual iefeis
isutyp expeiimental vaiiable foi each of the iesiuuals
vaityp type of potential paiametei to be optimizeu

S?PJ8& +/3X 5@*3/3X) ;30 6B5).+*) 95+ S`C;4+/H
166 "#$%&' ()*+,) -./0* 166

nauu numbei of auueu bonus between Z-matiix atoms
iauu numbeis of the atom paiis uefining auueu bonus
nuel numbei of bonus between Z-matiix bonus to uelete
iuel numbeis of the atom paiis uefining ueleteu bonus

S?JJ'I S`C;4+/H /34*+3;B 655+0/3;4* 0*9/3/4/53)

zbonu bonu length useu to uefine each Z-matiix atom
zang bonu angle useu to uefine each Z-matiix atom
ztois angle oi toision useu to uefine Z-matiix atom
iz uefining atom numbeis foi each Z-matiix atom

167 "#$%&' ()*+,) -./0* 167
112 #30*H 59 >.364/53 M8.A+5.4/3* ?;BB)
This section contains an alphabetical cioss inuex listing of the ioutines calleu by each TINKER
piogiam, subioutine anu function. Routines not piesent in this list uo not make calls to any othei
poition of the TINKER package.

'5.4/3* P/)4 59 85.+6* ?50* (3/4) 6;BB*0 AE 47/) '5.4/3*

N?"#Z& uETTEXT 0PCASE

NIIVN8& ABBB0NB FINBATN }AC0BI NEWATN 0LBATN
0vERLAP PIALTER PIN0vE PITILT

NII8#I& ABBBASE ABBB0NB FATAL FINBATN FREE0NIT
}AC0BI NEWATN 0LBATN 0vERLAP
PIALTER PIN0vE PITILT PRTSEQ
vERSI0N

NP?Y&OR ENERuY FINAL FREE0NIT uETTEXT uETXYZ
BAT0N BYBRIB INITIAL NECBANIC
N0NERAL REABXYZ 0PCASE vERSI0N

N$NPR8#8 B00NBS EANuANuS EANuLES EB0NBS EB0CKS
ECBARuES ECBuBPLS EBIP0LES EuA0SSS
EuE0NS EBALS EINPR0PS EINPT0RS
EL}S ENETALS ENNSBBS ENP0LES
E0PBENBS E0PBISTS EPIT0RSS ERXNFLBS
ES0LvS ESTRBNBS ESTRT0RS ET0RSS
ET0RT0RS E0REYS EXTRAS PISCF
REPLICA

N$NPRS& ANALYZ4 ANALYZ6 ANALYZ8 AT0NYZE ENRuYZE
FINAL FREE0NIT uETXYZ INITIAL
NECBANIC NEXTARu PARANYZE PR0PYZE
REABXYZ S0FFIX TRINTEXT 0PCASE
vERSI0N

N$-P&8 FATAL

N$$&NP BEENAN FINAL uETTEXT uETXYZ INITIAL
NBINIT NBREST NECBANIC NEXTARu
RuBSTEP SBSTEP SBAKE0P SIuN0IB
0PCASE vERLET


N'?Y#Z& ACTIvE BASEFILE FINAL FREE0NIT uETTEXT
INITIAL NEXTARu N0NERAL PRTARC
PRTCAR PRTXN0L PRTXYZ REABXYZ
S0FFIX TRINTEXT 0PCASE vERSI0N

168 "#$%&' ()*+,) -./0* 168
N""N?Y FATAL S0RT

VN8&>#P& C0NTR0L uETKEY TRINTEXT

V?(#$" BC0C0F

V?(#$"1 BC0C0F

V?(#$"D BC0C0F

V&&ON$ uRABIENT KINETIC NBSAvE NBSTAT PRESS0RE
RATTLE RATTLE2 TENPER TENPER2

V&"N# BETACF uANNLN

V#-VPJ?% CELLAT0N

V#"J'8 FATAL

VJ$I8 FATAL

VJ'$ S0RFAT0N

V8&" BNAX

V88"&G FATAL NNIB PZEXTR

?NP&$IN' BATE_ANB_TINE

?&''J' FATAL TRINTEXT

?>>"V CFFTB1

?>>"V1 PASSB PASSB2 PASSBS PASSB4 PASSBS

?>>"> CFFTF1

?>>">1 PASSF PASSF2 PASSFS PASSF4 PASSFS

?>>"# CFFTI1

?Y%"'&& L0CALXYZ

?#'GP$ AN0RN B0T vCR0SS vN0RN

?P#OV&' ENERuY uETREF L0CALNIN NAKEINT NAKEXYZ

?P#OV'-I ENERuY L0CALRuB RIuIBXYZ

169 "#$%&' ()*+,) -./0* 169
?P#OV'J" ENERuY L0CALR0T NAKEXYZ

?P#OV"J' CBKTREE ENERuY uETREF L0CALXYZ NAKEINT
NAKEXYZ

?P#OVQRS CBKTREE ENERuY uETREF L0CALXYZ

?P(8"&' C0T0FFS FATAL uETN0NB uETTEXT S0RT S0RTS
0PCASE

?JOON$I uETARu 0PCASE

?JOG'&88 CERR0R uETT0R

?J$$&?" S0RT

?J$$JPPR C0NPRESS C0NTACT NEIuBB0R PLACE SABBLES
T0R0S vAN

?J$"N?" AN0RN CERR0R PTINCY

?J$"'JP uETTEXT 0PCASE

?JJ'I8 uYRATE RNSERR0R

?J''&PN"& FINAL INITIAL NEXTARu PR0PERTY REABBLK
TRINTEXT

?'R8"NP BIuBL0CK B00NBS FIELB FINAL FREE0NIT
uETTEXT uETXYZ INITIAL KAT0N
LATTICE N0LEC0LE NEXTARu PRTXYZ
SYNNETRY 0NITCELL 0PCASE vERSI0N

?("J>>8 uETTEXT 0PCASE

?R"8R CYTSYP CYTSYS

I&G"Y B0T vCR0SS vN0RN

I#N-K uETINE SETINE

I#>>&K BSSTEP uBASTAT uvAL0E

I#>>(8& BASEFILE FATAL FIELB FINAL FREE0NIT
INITIAL KAT0N N0LEC0LE NEXTARu
REABXYZ S0FFIX 0NITCELL vERSI0N

I#8"-&JO ACTIvE ANuLES ATTACB B0NBS ENBEB
FATAL FINAL FREE0NIT uE0BESIC
uETINE uETTEXT uETXYZ uRAFIC
170 "#$%&' ()*+,) -./0* 170
INP0SE INITIAL KCBIRAL KuE0N
NAKEREF NEXTARu N0NERAL PRTXYZ
SETINE T0RSI0NS TRIFIX 0PCASE
vERSI0N

IOI(OG uRAFIC

IJ?(O&$" FINAL FREE0NIT uETPRN uETTEXT uETW0RB
INITIAL L0WCASE NEXTARu NEXTTEXT
PRTPRN S0RT1u S0RT6 S0RT7
S0FFIX TRINTEXT 0PCASE vERSI0N

I8"ON" uETINE uETN0NB uETTEXT INvBETA RANB0N
SETINE S0RT2 TRIFIX 0PCASE

IR$NO#? BEENAN FINAL uETXYZ INITIAL NBINIT
NBREST NECBANIC NEXTARu RuBSTEP
SBSTEP SBAKE0P vERLET

&N$-N$- uR00PS INAuE

&N$-N$-1 uR00PS INAuE

&N$-N$-D EANuANu2A uR00PS

&N$-N$-DN INAuE

&N$-N$-L uR00PS INAuE

&N$-P& uR00PS INAuE

&N$-P&1 uR00PS INAuE

&N$-P&D EANuLE2A EANuLE2B uR00PS

&N$-P&DN uR00PS INAuE

&N$-P&DV INAuE

&N$-P&L uR00PS INAuE

&VJ$I uR00PS INAuE

&VJ$I1 uR00PS INAuE

&VJ$ID uR00PS INAuE

&VJ$IL uR00PS INAuE

&V(?% EB0CKuA EB0CKuB EB0CKuC FATAL
171 "#$%&' ()*+,) -./0* 171

&V(?%TN uR00PS INAuE SWITCB

&V(?%TV uR00PS LIuBTS SWITCB

&V(?%T? EuA0SS

&V(?%1 EB0CK1A EB0CK1B EB0CK1C FATAL

&V(?%1N uR00PS INAuE SWITCB

&V(?%1V uR00PS LIuBTS SWITCB

&V(?%1? EuA0SS1

&V(?%D EB0CK2A EB0CK2B FATAL

&V(?%DN uR00PS INAuE SWITCB

&V(?%DV EuA0SS2

&V(?%L EB0CKSA EB0CKSB EB0CKSC FATAL

&V(?%LN uR00PS INAuE SWITCB

&V(?%LV uR00PS LIuBTS SWITCB

&V(?%L? EuA0SSS

&?YN'-& ECBARuEuA ECBARuEuB ECBARuEuC ECBARuEuB ECBARuEuE

&?YN'-&TN uR00PS INAuE SWITCB

&?YN'-&TV uR00PS LIuBTS SWITCB

&?YN'-&T? ERF uR00PS

&?YN'-&TI EPNE ERFC uR00PS INAuE SWITCB

&?YN'-&T& EPNE ERFC uR00PS LIuBTS SWITCB

&?YN'-&1 ECBARuE1A ECBARuE1B ECBARuE1C ECBARuE1B

&?YN'-&1N uR00PS INAuE SWITCB

&?YN'-&1V uR00PS LIuBTS SWITCB

&?YN'-&1? ERF uR00PS

172 "#$%&' ()*+,) -./0* 172
&?YN'-&1I EPNE1 ERFC uR00PS INAuE SWITCB

&?YN'-&D ECBARuE2A ECBARuE2B ECBARuE2C

&?YN'-&DN uR00PS INAuE SWITCB

&?YN'-&DV ERF uR00PS

&?YN'-&D? ERFC uR00PS INAuE

&?YN'-&L ECBARuESA ECBARuESB ECBARuESC ECBARuESB ECBARuESE

&?YN'-&LN uR00PS INAuE SWITCB

&?YN'-&LV uR00PS LIuBTS SWITCB

&?YN'-&L? ERF uR00PS

&?YN'-&LI EPNES ERFC uR00PS INAuE SWITCB

&?YN'-&L& EPNES ERFC uR00PS LIuBTS SWITCB

&?Y-IGP uR00PS INAuE SWITCB

&?Y-IGP1 uR00PS INAuE SWITCB

&?Y-IGPD uR00PS INAuE SWITCB

&?Y-IGPL uR00PS INAuE SWITCB

&I#GJP& uR00PS INAuE SWITCB

&I#GJP&1 uR00PS INAuE SWITCB

&I#GJP&D uR00PS INAuE SWITCB

&I#GJP&L uR00PS INAuE SWITCB

&-N(88 EuA0SSuA EuA0SSuB

&-N(88TN uR00PS SWITCB

&-N(88TV ERF uR00PS

&-N(881 EuA0SS1A EuA0SS1B

&-N(881N uR00PS SWITCB

&-N(881V ERF uR00PS
173 "#$%&' ()*+,) -./0* 173

&-N(88D EuA0SS2A EuA0SS2B

&-N(88DN uR00PS SWITCB

&-N(88DV uR00PS

&-N(88L EuA0SSSA EuA0SSSB

&-N(88LN uR00PS SWITCB

&-N(88LV ERF uR00PS

&-V8NTN uR00PS SWITCB

&-V8NTV ERF uR00PS

&-V8N1N uR00PS SWITCB

&-V8N1V ERF uR00PS

&-V8NDN SWITCB

&-V8NDV ERF

&-V8NLN uR00PS SWITCB

&-V8NLV ERF uR00PS

&-&JO uR00PS INAuE

&-&JO1 uR00PS INAuE

&-&JOD uR00PS INAuE

&-&JOL uR00PS INAuE

&YNP EBALuA EBALuB

&YNPTN uR00PS INAuE SWITCB

&YNPTV uR00PS LIuBTS SWITCB

&YNP1 EBAL1A EBAL1B

&YNP1N uR00PS INAuE SWITCB

&YNP1V uR00PS LIuBTS SWITCB

174 "#$%&' ()*+,) -./0* 174
&YNPD uR00PS INAuE SWITCB

&YNPL EBALSA EBALSB

&YNPLN uR00PS INAuE SWITCB

&YNPLV uR00PS LIuBTS SWITCB

&#-&$ uETINE P0WER SETINE

&#-&$'-I BIAuQ BESSRuB

&#-&$'J" BIAuQ BESSR0T

&#-&$'J" BIAuQ BESSR0T

&#-&$"J' BIAuQ BESSR0T

&#-&$QRS BIAuQ BESSIAN

&#OG'JG uR00PS INAuE

&#OG'JG1 uR00PS INAuE

&#OG'JGD uR00PS INAuE

&#OG'JGL uR00PS INAuE

&#OG"J' uR00PS INAuE

&#OG"J'1 uR00PS INAuE

&#OG"J'D uR00PS INAuE

&#OG"J'L uR00PS INAuE

&Pe EL}uA EL}uB EL}uC EL}uB

&PeTN uR00PS INAuE SWITCB

&PeTV uR00PS LIuBTS SWITCB

&PeT? EuA0SS

&PeTI uR00PS

&Pe1 EL}1A EL}1B EL}1C EL}1B

&Pe1N uR00PS INAuE SWITCB
175 "#$%&' ()*+,) -./0* 175

&Pe1V uR00PS LIuBTS SWITCB

&Pe1? EuA0SS1

&Pe1I uR00PS

&PeD EL}2A EL}2B

&PeDN uR00PS INAuE SWITCB

&PeDV EuA0SS2

&PeD? uR00PS

&PeL EL}SA EL}SB EL}SC EL}SB

&PeLN uR00PS INAuE SWITCB

&PeLV uR00PS LIuBTS SWITCB

&PeL? EuA0SSS

&PeLI uR00PS

&OV&I BNBERR CBIRER CBKSIZE C00RBS BNB0NP
BSTNAT EIuEN EXPL0RE FRACBIST
FREE0NIT uETINE uYRATE INP0SE
L0CERR NA}0RIZE NETRIC N0NERAL
PRTXYZ REFINE RNSERR0R SETINE
T0RSER vBWERR

&O&"NP FATAL

&O&"NP1 FATAL

&O&"NPL ENETAL

&OOLYV ENNSBBuA ENNSBBuB

&OOLYVTN uR00PS INAuE SWITCB

&OOLYVTV uR00PS LIuBTS SWITCB

&OOLYV1 ENNSBB1A ENNSBB1B

&OOLYV1N uR00PS INAuE SWITCB

&OOLYV1V uR00PS LIuBTS SWITCB
176 "#$%&' ()*+,) -./0* 176

&OOLYVD uR00PS INAuE SWITCB

&OOLYVL ENNSBBSA ENNSBBSB

&OOLYVLN uR00PS INAuE SWITCB

&OOLYVLV uR00PS LIuBTS SWITCB

&OGJP& ENP0LEuA ENP0LEuB

&OGJP&TN CBKP0LE uR00PS INAuE INB0CE R0TP0LE
SWITCB

&OGJP&TV CBKP0LE EREAL ERECIP INB0CE R0TP0LE

&OGJP&1 ENP0LE1A ENP0LE1B

&OGJP&1N CBKP0LE uR00PS INAuE INB0CE R0TP0LE
SWITCB T0RQ0E T0RQ0E1

&OGJP&1V CBKP0LE EREAL1 ERECIP1 INB0CE R0TP0LE
T0RQ0E

&OGJP&D ENP0LE2A

&OGJP&DN uR00PS INAuE SWITCB T0RQ0E

&OGJP&L ENP0LESA ENP0LESB

&OGJP&LN CBKP0LE uR00PS INAuE INB0CE R0TP0LE
SWITCB

&OGJP&LV CBKP0LE EREALS ERECIPS INB0CE R0TP0LE

&$&'-R B00NBS EANuANu EANuLE EB0NB EB0CK
ECBARuE ECBuBPL EBIP0LE EuA0SS
EuE0N EBAL EINPR0P EINPT0R
EL} ENETAL ENNSBB ENP0LE
E0PBENB E0PBIST EPIT0RS ERXNFLB
ES0Lv ESTRBNB ESTRT0R ET0RS
ET0RT0R E0REY EXTRA PISCF
REPLICA

&$'-RS& ANALYSIS

&JGV&$I uR00PS INAuE

&JGV&$I1 uR00PS INAuE

177 "#$%&' ()*+,) -./0* 177
&JGV&$ID E0PBENB2A uR00PS

&JGV&$IDN INAuE

&JGV&$IL uR00PS INAuE

&JGI#8" uR00PS INAuE

&JGI#8"1 uR00PS INAuE

&JGI#8"D uR00PS INAuE

&JGI#8"L uR00PS INAuE

&G#"J'8 uR00PS INAuE

&G#"J'81 uR00PS INAuE

&G#"J'8D EPIT0RS2A uR00PS

&G#"J'8DN INAuE

&G#"J'8L uR00PS INAuE

&GO& BSPLINE FFTFR0NT

&GO&1 BSPLINE1 FFTBACK FFTFR0NT

&GO&L BSPLINE FFTFR0NT

&G(?P? AN0RN

&'&NP ERFC INAuE SWITCB

&'&NP1 ERFC INAuE SWITCB T0RQ0E T0RQ0E1

&'&NPL ERFC INAuE SWITCB

&'&?#G1 T0RQ0E

&'> ERFC0RE

&'>? ERFC0RE

&'>#% B1B2 RFINBEX

&'>#$Z ERF FATAL

&'Q$>PI CBKP0LE ERFIK I}KPTS R0TP0LE SWITCB
178 "#$%&' ()*+,) -./0* 178

&'Q$>PIL CBKP0LE ERFIK I}KPTS R0TP0LE SWITCB

&8JPZ B0RN EuBSAuA EuBSAuB S0RFACE

&8JPZ1 B0RN B0RN1 EuBSA1A EuBSA1B S0RFACE

&8JPZD EuBSA2A EuBSA2B

&8JPZL B0RN EuBSASA EuBSASB S0RFACE

&8"'V$I uR00PS INAuE

&8"'V$I1 uR00PS INAuE

&8"'V$ID uR00PS INAuE

&8"'V$IL uR00PS INAuE

&8"'"J' uR00PS INAuE

&8"'"J'1 uR00PS INAuE

&8"'"J'D uR00PS INAuE

&8"'"J'L uR00PS INAuE

&"J'8 ET0RSuA ET0RSuB

&"J'8TN uR00PS INAuE

&"J'8TV uR00PS

&"J'81 ET0RS1A ET0RS1B

&"J'81N uR00PS INAuE

&"J'81V uR00PS

&"J'8D ET0RS2A ET0RS2B

&"J'8DN uR00PS INAuE

&"J'8DV uR00PS

&"J'8L ET0RSSA ET0RSSB

&"J'8LN uR00PS INAuE

179 "#$%&' ()*+,) -./0* 179
&"J'8LV uR00PS

&"J'"J' BC0INT uR00PS INAuE

&"J'"J'1 BC0INT1 uR00PS INAuE

&"J'"J'D BC0INT2 uR00PS INAuE

&"J'"J'L BC0INT uR00PS INAuE

&('&R uR00PS INAuE

&('&R1 uR00PS INAuE

&('&RD uR00PS INAuE

&('&RL uR00PS INAuE

&<NPI?J> ERFC

&QGPJ'& INITERR NIBERR SIuN0IB T0TERR

>>"VN?% CFFTB

>>">'J$" CFFTF

>>"8&"(G CFFTI

>#&PI uETPRN PRNKEY

>#$NP SKTKILL

>'N?I#8" BIST2 TRINTEXT

>'&&($#" FATAL

-IN BIFFEQ FINAL FREE0NIT uBASTAT uETTEXT
uETXYZ INITIAL NECBANIC NEXTARu
N0NERAL PRTXYZ RANB0N TNCu 0PCASE
vERSI0N

-IN1 uRABIENT BESSIAN

-IND uRABIENT

-INL BESSIAN

-IN8"N" ENERuY uYRATE 0PTSAvE

180 "#$%&' ()*+,) -./0* 180
-&JI&8#? NINPATB S0RTS

-&"VN8& PBBATN

-&"#O& CL0CK

-&"#$" BASEFILE CBKXYZ C0NNECT FATAL FREE0NIT
NAKEXYZ NEXTARu REABINT S0FFIX
vERSI0N

-&"%&R FATAL FREE0NIT uETTEXT S0FFIX TRINTEXT
0PCASE

-&"OJPD BASEFILE FREE0NIT NEXTARu REABN0L2 S0FFIX
vERSI0N

-&"$(?Y PBBATN

-&"$(OV TRINTEXT

-&"GIV BASEFILE FREE0NIT NEXTARu REABPBB S0FFIX
vERSI0N

-&"G'V BIST2 B0T uETT0R vCR0SS

-&"G'O FATAL FREE0NIT uETTEXT INITPRN NEXTARu
REABPRN S0FFIX TRINTEXT 0PCASE
vERSI0N

-&"G'JY PBBATN

-&"8&K uETW0RB TRINTEXT 0PCASE

-&"8&K$ uETTEXT uETW0RB TRINTEXT 0PCASE

-&"8#I& PBBATN

-&""J' BIST2

-&"QRS BASEFILE FATAL FREE0NIT NEXTARu REABXYZ
S0FFIX vERSI0N

-'NI#&$" B00NBS EANuANu1 EANuLE1 EB0NB1 EB0CK1
ECBARuE1 ECBuBPL1 EBIP0LE1 EuA0SS1
EuE0N1 EBAL1 EINPR0P1 EINPT0R1
EL}1 ENETAL1 ENNSBB1 ENP0LE1
E0PBENB1 E0PBIST1 EPIT0RS1 ERXNFLB1
ES0Lv1 ESTRBNB1 ESTRT0R1 ET0RS1
ET0RT0R1 E0REY1 EXTRA1 PISCF
REPLICA
181 "#$%&' ()*+,) -./0* 181

-'NI'-I uRABIENT

-'NI'J" uRABIENT R0TLIST

YN$-P& N0NERAL

YVJ$I N0NERAL

YI#GJP& N0NERAL

Y&88#N$ B0RN B00NBS CBKP0LE EANuANu2 EANuLE2
EB0NB2 EB0CK2 ECBARuE2 ECBuBPL2
EBIP0LE2 EuA0SS2 EuE0N2 EBAL2
EINPR0P2 EINPT0R2 EL}2 ENETAL2
ENNSBB2 ENP0LE2 E0PBENB2 E0PBIST2
EPIT0RS2 ERXNFLB2 ES0Lv2 ESTRBNB2
ESTRT0R2 ET0RS2 ET0RT0R2 E0REY2
EXTRA2 FATAL INB0CE PISCF
REPLICA R0TP0LE

Y&88'-I uRABRuB RIuIBXYZ

Y&88'J" uRABR0T NAKEXYZ

Y#OG"J' N0NERAL

Y8"'"J' N0NERAL

Y"J'8 N0NERAL

YRV'#I BANuLE BAT0N BB0NB BCBARuE BBIP0LE
BINPT0R BSTRBNB BSTRT0R BT0RS
BvBW

#OGJ8& CENTER Q0ATFIT RNSFIT

#$I(?& INB0CEuA INB0CEuB

#$I(?&TN FATAL uR00PS INAuE PRTERR SWITCB

#$I(?&TV FATAL PRTERR 0BIRECT1 0BIRECT2 0N0T0AL1
0N0T0AL2

#$&I-& CERR0R

#$&'"#N }AC0BI

#$#"&'' L0CERR T0RSER

182 "#$%&' ()*+,) -./0* 182
#$#"#NP C0NNANB INITRES PRECISE PR0N0

#$#"'J" FATAL NEXTARu R0TCBECK R0TLIST

#$"&I#" FIELB FINAL FREE0NIT uE0NETRY uETINT
uETW0RB INITIAL NAKEXYZ N0NBER
PRTINT TRINTEXT 0PCASE vERSI0N
ZBELP ZvAL0E

#$"QRS FINAL FREE0NIT uETINT INITIAL PRTXYZ
vERSI0N

#$ZV&"N BETAI uANNLN

#$Z&'" FATAL

#G&I-& CERR0R

#8GPG& CYTSY CYTSYS

%N$-N$- uETTEXT 0PCASE

%N$-P& uETTEXT N0NERAL 0PCASE

%N"JO uETN0NB uETSTRINu uETTEXT 0PCASE

%VJ$I uETTEXT KENEu N0NERAL 0PCASE

%?YN'-& uETTEXT 0PCASE

%I#GJP& uETTEXT N0NERAL 0PCASE

%&$&- uETTEXT N0NERAL 0PCASE

%&<NPI EWALBC0F FATAL FFTSET0P uETTEXT N0B0LI
0PCASE

%-&JO FATAL uE0NETRY uETTEXT uETW0RB INAuE
0PCASE

%#OG'JG uETTEXT N0NERAL 0PCASE

%#OG"J' uETTEXT N0NERAL T0RPBASE 0PCASE

%OGJP& CBKP0LE uETTEXT N0NBER N0NERAL RANB0N
S0RTS 0PCASE

%JGV&$I uETTEXT N0NBER N0NERAL 0PCASE

183 "#$%&' ()*+,) -./0* 183
%JGI#8" uETTEXT N0NERAL 0PCASE

%J'V#" uETTEXT N0NERAL 0PCASE

%G#"J'8 uETTEXT N0NERAL 0PCASE

%GJPN' CBKP0LE uETTEXT P0LARuRP 0PCASE

%8JPZ uETTEXT uETW0RB KANuLE KB0NB 0PCASE

%8"'V$I uETTEXT 0PCASE

%8"'"J' uETTEXT N0NERAL 0PCASE

%"J'8 uETTEXT N0NERAL T0RPBASE 0PCASE

%"J'"J' uETTEXT ISPLPE N0NERAL S0RT9 0PCASE

%('&R uETTEXT N0NERAL 0PCASE

%ZI< uETTEXT N0NBER N0NERAL 0PCASE

PV>-8 C0NNENT' uETTEXT 0PTSAvE SEARCB 0PCASE

P#-N8& FINBATN

P#-Y"8 FATAL S0RT2 S0RTS

PO8"&G PRECISE QRS0LvE

PJ?NPO#$ uRABIENT TNCu

PJ?NP'-I 0CvN

PJ?NP'J" 0CvN

PJ?NPQRS TNCu

ONeJ'#S& uETINE uYRATE RNSERR0R SETINE

ON%&#$" AB}ACENT FATAL uE0NETRY uETTEXT 0PCASE

ON%&GIV ATTACB FREE0NIT uETBASE uETN0CB uETPR0B
uETSIBE N0NERAL PBBATN REABSEQ
vERSI0N

ON%&QRS XYZATN

ONG?Y&?% FREE0NIT N0NERAL PRTXYZ vERSI0N
184 "#$%&' ()*+,) -./0* 184

ONQ<&PP ERFINv RANB0N

O?O1 uRABIENT

O?OD BESSIAN

O?O8"&G TNCu

OI#$#" FREE0NIT uETTEXT uETW0RB uRABIENT uRPLINE
LATTICE NAXWELL NBREST N0NERAL
RANvEC REABBYN 0PCASE vERSI0N

OI'&8" INvERT

OI8NZ& FATAL FREE0NIT N0NERAL 0PENENB PRTBYN
PRTXYZ SKTBYN S0FFIX TRINTEXT
vERSI0N

O&N8>$ CERR0R TRIPLE vCR0SS vECANu vN0RN

O&N8>G CERR0R B0T vCR0SS vECANu vN0RN

O&N8>8 CERR0R B0T vECANu vN0RN

O&N8GO vCR0SS

O&?YN$#? ACTIvE ANuLES ATTACB BIT0RS B0NBS
CL0STER C0T0FFS FATAL FIELB
KANuANu KANuLE KAT0N KB0NB
KCBARuE KBIP0LE KEWALB KuE0N
KINPR0P KINPT0R KNETAL KNP0LE
K0PBENB K0PBIST K0RBIT KPIT0RS
KP0LAR KS0Lv KSTRBNB KSTRT0R
KT0RS KT0RT0R K0REY KvBW
LATTICE N0LEC0LE N0TATE 0RBITAL
P0LYNER RINuS SN00TB T0RSI0NS
0NITCELL

O&'-& FATAL uETREF

O#I&'' BNBERR CBIRER L0CERR T0RSER

O#$#O#S1 uRABIENT

O#$#O#S& FINAL FREE0NIT uETTEXT uETXYZ uRABIENT
INITIAL LBFuS NECBANIC NEXTARu
PRTXYZ 0PCASE vERSI0N

185 "#$%&' ()*+,) -./0* 185
O#$#'J" FINAL FREE0NIT uETINT uETTEXT uRABR0T
INITIAL INITR0T LBFuS NECBANIC
NEXTARu PRTINT 0PCASE vERSI0N

O#$#'J"1 uRABR0T NAKEXYZ

O#$'#-#I FINAL FREE0NIT uETTEXT uETXYZ uRABRuB
INITIAL LBFuS NECBANIC NEXTARu
0RIENT PRTXYZ 0PCASE vERSI0N

O#$'#-#I1 uRABRuB RIuIBXYZ

OO#I uvAL0E

OJI&?N'" CLINBXYZ EIuENXYZ uETREF INP0SE NAKEREF

OJI&'J" CLINBR0T EIuENR0T NAKEXYZ

OJI&8'?Y CLINBER EIuENR0T NAKEINT NAKEREF NAPCBECK

OJI&"J'8 CLINBT0R EIuENT0R uETREF INP0SE NAKEINT
NAKEREF

OJI(P# BSPLINE BFTN0B

OJP&?(P& S0RT S0RTS

OJP(#$I 0FIELB

OJO&$"8 CBKP0LE INB0CE }AC0BI R0TP0LE

OJ$"& CBKCLASB FREE0NIT uETREF uETTEXT uETXYZ
INITIAL INITR0T NAKEINT NAKEREF
NAKEXYZ NCNSTEP NECBANIC NEXTARu
PRTXYZ RANB0N RANvEC 0PCASE
vERSI0N

O("N"& uETTEXT 0PCASE

$&#-YVJ' CERR0R BIST2

$&<N"O ABBB0NB XYZATN

$&<"J$ FINAL FREE0NIT uETTEXT uETXYZ uRABIENT
INITIAL NECBANIC NEXTARu PRTXYZ
TNCu 0PCASE vERSI0N

$&<"J$1 uRABIENT

$&<"J$D BESSIAN
186 "#$%&' ()*+,) -./0* 186

$&<"'J" FINAL FREE0NIT uETINT uETTEXT uRABR0T
INITIAL INITR0T NECBANIC NEXTARu
PRTINT TNCu 0PCASE vERSI0N

$&<"'J"1 uRABR0T NAKEXYZ

$&<"'J"D BESSR0T NAKEXYZ

$J'ONP RANB0N

$(?VN8& 0CvN 0RIENT P0T0FF ZAT0N

$(??YN#$ N0CBASE 0CvN 0RIENT ZAT0N

$(?P&#? BASEFILE C0NNECT BELETE FIELB FREE0NIT
uETKEY uETSEQN INITIAL NAKEINT
NAKEXYZ N0LEC0LE NEXTARu N0CCBAIN
PRTINT PRTSEQ PRTXYZ TRINTEXT
vERSI0N WATS0N

$(OV&' TRINTEXT

J?ZO uETTEXT 0PTSAvE PRECISE 0PCASE

JPIN"O ABBB0NB FATAL

JG"#O#S1 uRABIENT

JG"#O#S& FATAL FINAL FREE0NIT uETTEXT uETXYZ
uRABIENT INITIAL NECBANIC NEXTARu
0CvN PRTXYZ 0PCASE vERSI0N

JG"#'J" FATAL FINAL FREE0NIT uETINT uETTEXT
uRABR0T INITIAL INITR0T NECBANIC
NEXTARu 0CvN PRTINT 0PCASE
vERSI0N

JG"#'J"1 uRABR0T NAKEXYZ

JG"'#-#I FATAL FINAL FREE0NIT uETTEXT uETXYZ
uRABRuB INITIAL NECBANIC NEXTARu
0CvN 0RIENT PRTXYZ 0PCASE
vERSI0N

JG"'#-#I1 uRABRuB RIuIBXYZ

JG"8NZ& FATAL FREE0NIT NAKEXYZ N0NERAL 0PENENB
PRTINT PRTXYZ SKT0PT S0FFIX
vERSI0N
187 "#$%&' ()*+,) -./0* 187

J'V#"NP FATAL uETTEXT PIPLANE 0PCASE

J'#&$" XYZRIuIB

JZ&'PNG SLATER

GN"Y FINAL uETXYZ INP0SE INITIAL INvERT
LBFuS NECBANIC NEXTARu 0PTSAvE
0RTB0u P0TNRu

GN"Y1 P0TNRu

GN"YG$" 0CvN

GN"Y8?N$ PATBPNT SABBLE1 TANuENT

GN"YZNP INP0SE

GIVQRS CBKXYZ BELETE FIELB FINAL FREE0NIT
uETN0NB uETPBB INITIAL LIuASE
PRTXYZ RIB0S0NE S0RT 0PCASE
vERSI0N

G#GPN$& FATAL

G#8?> NEWATN

G#"#P" 0LBATN

GPN?& CERR0R BIST2 uETPRB uETT0R INEBuE

GJPN'-'G S0RT S0RT8

GJPN'#S& FATAL uETXYZ INITIAL }AC0BI NECBANIC
N0L0INB

GJPRO&' FATAL uETTEXT INAuE 0PCASE

GJ"$'- uRABIENT

GJ<&' RANB0N

G'&?J$I CB0LESKY C0L0NN

G'&88('& LATTICE

G'O%&R uETTEXT uETW0RB P0T0FF 0PCASE

188 "#$%&' ()*+,) -./0* 188
G'J?YN#$ uETTEXT PR0SIBE 0PCASE ZAT0N

G'Je?" B0T

G'JGRS& uRABIENT uYRATE INERTIA N0NENTS

G'J8#I& FREE0NIT PRTINT PRTXYZ vERSI0N ZAT0N

G'J"&#$ BASEFILE CBKXYZ C0NNECT BELETE FIELBFINAL
FREE0NIT uETKEY uETSEQ INITIAL
NAKEINT NAKEXYZ NEXTARu PR0CBAIN
PRTINT PRTSEQ PRTXYZ TRINTEXT
vERSI0N

G'"N'? vERSI0N

G'"?N' vERSI0N

G'"IR$ ZAT0N

G'"&'' ZAT0N

G'"#$" vERSI0N

G'"OJPD N0NBER vERSI0N

G'"GIV vERSI0N

G'"G'O N0NBER

G'"8&K vERSI0N

G'"QOJP vERSI0N

G'"QRS vERSI0N

G88 ACTIvE FINAL uETTEXT uETXYZ INP0SE
INITIAL INITR0T L0CALXYZ NAKEINT
NAKEREF NECBANIC N0BECART N0BET0RS
NEXTARu PSSWRITE SIuN0IB 0PCASE

G881 uRABIENT

G88D BESSIAN

G88'-I1 uRABRuB RIuIBXYZ

G88'#-#I FINAL FREE0NIT uETTEXT uETXYZ INP0SE
INITIAL NAKEREF NECBANIC NEXTARu
N0NERAL 0CvN 0RIENT PRTXYZ
189 "#$%&' ()*+,) -./0* 189
RuBSRCB RIuIBXYZ SIuN0IB 0PCASE
vERSI0N

G88'J" FINAL FREE0NIT uETTEXT uETXYZ INP0SE
INITIAL INITR0T NAKEREF NAKEXYZ
NECBANIC N0BER0T NEXTARu N0NERAL
0CvN PRTXYZ 0PCASE vERSI0N

G88'J"1 uRABR0T NAKEXYZ

G88<'#"& FREE0NIT N0NERAL PRTXYZ vERSI0N

G"#$?R B0T EP0CLC PR0}CT R0TANu

K(N">#" }AC0BI

'NI#NP BASEFILE FATAL FINAL FREE0NIT uETTEXT
uETW0RB INAuE INITIAL LATTICE
N0LEC0LE NEXTARu REABXYZ S0FFIX
0NITCELL 0PCASE vERSI0N

'N$IJO CALENBAR uETTEXT 0PCASE

'N$Z&? RANB0N

'N""P& FATAL INAuE PRTERR

'N""P&D FATAL INAuE PRTERR

'&NIVP% FATAL FREE0NIT uETW0RB N0NERAL

'&NIIR$ FATAL vERSI0N

'&NI#$" FATAL uETTEXT uETW0RB NEXTTEXT TRINTEXT
vERSI0N

'&NIOJPD FATAL uETTEXT uETW0RB S0RT TRINTEXT
0PCASE vERSI0N

'&NIGIV FATAL FIXPBB uETTEXT NEXTARu TRINTEXT
0PCASE vERSI0N

'&NIG'O FATAL uETN0NB uETSTRINu uETTEXT uETW0RB
N0NERAL PRNKEY S0RT9 T0RPBASE
TRINTEXT 0PCASE

'&NI8&K FATAL uETN0NB uETTEXT uETW0RB TRINTEXT
vERSI0N

190 "#$%&' ()*+,) -./0* 190
'&NIQRS CBKXYZ FATAL uETTEXT uETW0RB NEXTTEXT
S0RT TRINTEXT vERSI0N

'&>#$& LBFuS

'&GP#?N FATAL

'-I8'?Y CLINBRuB EIuENRuB RIuIBXYZ

'-I8"&G CB0LESKY uRABIENT KINETIC LINB0BY NBSAvE
NBSTAT PRESS0RE R0TRuB TENPER2

'#VJ8JO& ABBB0NB ABBSIBE FATAL FINBATN FREE0NIT
NEWATN 0LBATN PRTSEQ vERSI0N

'#$-8 ANuLES BIT0RS B0NBS FATAL T0RSI0NS

'O8&''J' TRINTEXT

'J"N$- B0T vCR0SS

'J"?Y&?% R0TLIST

'J"P#8" FATAL

'J"GJP& R0TNAT R0TSITE

8NIIP& C0NNENT' FATAL FINAL FREE0NIT uETTEXT
uETXYZ INP0SE INITIAL NAKEINT
NAKEXYZ NECBANIC NEXTARu PATBPNT
PATBSCAN PATBvAL PRTXYZ REABXYZ
SABBLE1 SEARCB TANuENT 0PCASE
vERSI0N

8NIIP&1 uRABIENT

8NIIP&8 CERR0R IPEBuE TRIPLE

8?N$ ACTIvE FINAL FREE0NIT uETXYZ INITIAL
INITR0T L0CALNIN NAKEINT NAPCBECK
NECBANIC N0BESRCB NEXTARu N0NERAL
REABXYZ vERSI0N

8?N$1 uRABIENT

8?N$D BESSIAN

8IN'&N S0RFAT0N

191 "#$%&' ()*+,) -./0* 191
8I8"&G uRABIENT KINETIC NBSAvE NBSTAT PRESS0RE
RATTLE RATTLE2 SBTERN

8I"&'O N0RNAL SBAREA

8&"#O& CL0CK

8YN%&(G CBKRINu uETN0NB uETTEXT uETW0RB 0PCASE

8%"IR$ CREATE0PBATE uETN0NIT0R NEEB0PBATE
RELEASEN0NIT0R SETACCELERATI0N
SETC00RBINATES SETENERuY
SETINB0CEB SETTINE SET0PBATEB
SETvEL0CITY SKTINIT

8%"#$#" CREATE}vN CREATESERvERCREATESYSTENSETAT0NIC
SETAT0NTYPESSETCBARuE
SETC0NNECTIvITY SETC00RBINATES
SETFILE SETF0RCEFIELB SETKEYW0RB
SETNASS SETNANE SETST0RY

8%"%#PP BESTR0Y}vN BESTR0YSERvER SKTBYN SKT0PT

8%"JG" CREATE0PBATE uETN0NIT0R NEEB0PBATE
RELEASEN0NIT0R SETC00RBINATES
SETENERuY SETuRABIENTS SETINB0CEB
SETSTEP SET0PBATEB SKTINIT

8PN"&' ASET BSET C}KN P0LYP

8OJJ"Y uETTEXT uETW0RB NEXTARu 0PCASE

8$#>>&' FINAL FREE0NIT uETREF uETXYZ uRABIENT
INITIAL NAKEREF NECBANIC NEXTARu
0PTSAvE PRTXYZ SNIFFER1 vERSI0N

8$#>>&'1 uRABIENT

8JN% BELETE FREE0NIT INAuE LATTICE NAKEREF
NERuE N0LEC0LE REABXYZ S0FFIX
0NITCELL vERSI0N

8GN?&>#PP ACTIvE C0NN0LLY FIELB FINAL FREE0NIT
uETTEXT uETXYZ INITIAL KAT0N
KvBW NEXTARu REABXYZ S0FFIX
0PCASE vERSI0N

8G&?"'(O BASEFILE FREE0NIT INITIAL NEXTARu S0FFIX
vERSI0N

192 "#$%&' ()*+,) -./0* 192
8K(N'& uETTEXT LNSTEP LSQWRITE PRECISE QRFACT
RSBvAL0E TR0ST 0PCASE

8(>>#Q TRINTEXT

8(G&'GJ8& FIELB FINAL FREE0NIT uETTEXT uETXYZ
INP0SE INITIAL KAT0N NEXTARu
PRTXYZ REABXYZ S0FFIX TRINTEXT
0PCASE vERSI0N

8('>N?& FATAL S0RT2

8('>N"JO FATAL S0RT2

8<#"?Y REPLICA

8RVRPQRS FINAL FREE0NIT uETN0L2 INITIAL PRTXYZ
vERSI0N

8ROO&"'R CELLAT0N

"N$-&$" PATBPNT SABBLE1

"&OG&' KINETIC

"&OG&'D NAXWELL RANB0N RANvEC

"&8"-'NI ENERuY FINAL uETTEXT uETXYZ uRABIENT
INITIAL NECBANIC NEXTARu 0PCASE

"&8"Y&88 FINAL FREE0NIT uETTEXT uETXYZ uRABIENT
BESSIAN INITIAL NECBANIC NEXTARu
N0NuRAB 0PCASE vERSI0N

"&8"P#-Y" EB0CK EB0CK1 ECBARuE ECBARuE1 EuA0SS
EuA0SS1 EBAL EBAL1 EL} EL}1
ENNSBB ENNSBB1 FINAL uETINE
uETXYZ INITIAL LIuBTS NECBANIC
NEXTARu SETINE

"&8"'J" ENERuY FINAL uETINT uRABR0T INITIAL
INITR0T NAKEXYZ NECBANIC NEXTARu

"#O&' ENERuY FINAL uETINE uETTEXT uETXYZ
uRABIENT BESSIAN INITIAL NECBANIC
NEXTARu SETINE 0PCASE

"#O&'J" ENERuY FINAL uETINE uETINT uETTEXT
uRABR0T BESSR0T INITIAL INITR0T
NECBANIC NEXTARu SETINE 0PCASE
193 "#$%&' ()*+,) -./0* 193

"$?- uETTEXT BNATRIX 0PTSAvE PISCF SEARCB
TNS0LvE 0PCASE

"$8JPZ& PREC0NB

"J'8#J$8 FATAL

"J'(8 CERR0R uETT0R

"J"&'' BNBERR CBIRER L0CERR T0RSER vBWERR

"'#N$-P& FATAL

"'#GP& B0T vCR0SS

"'(8" PRECISE RSBvAL0E

(I#'&?"D ERFC INAuE SWITCB

(O("(NPD ERFC INAuE SWITCB

($#"?&PP FATAL uETTEXT uETW0RB 0PCASE

ZNO CERR0R CIRPLN BEPTB BIST2 B0T
uENB0T NEASFN NEASFP NEASFS
NEASPN TRIPLE vCR0SS vN0RN

ZI<&'' LIuBTS

Z&?N$- AN0RN B0T TRIPLE

Z&'P&" uRABIENT KINETIC NBSAvE NBSTAT PRESS0RE
RATTLE RATTLE2 TENPER TENPER2

Z&'8#J$ L0WCASE NEXTARu TRINTEXT

Z#V'N"& BIAuQ FATAL FINAL FREE0NIT uETXYZ
BESSIAN INITIAL NECBANIC NEXTARu
N0NERAL PRTXYZ vERSI0N

Z#V'#-#I BIAuQ FINAL uETXYZ BESSRuB INITIAL
NECBANIC 0RIENT

Z#V'J" BIAuQ FINAL uETINT BESSR0T INITIAL
INITR0T NECBANIC

Z$J'O AN0RN

194 "#$%&' ()*+,) -./0* 194
ZJP(O& C0NN0LLY

ZJP(O&1 FATAL

ZJP(O&D FATAL

<N"8J$ ZAT0N

<N"8J$1 uRABRuB RIuIBXYZ

Q"NP&'' ENERuY XTALN0vE XTALPRN

Q"NP>#" FINAL uETXYZ INITIAL NECBANIC NEXTARu
P0T0FF SQ0ARE XTALPRN

Q"NPPN"1 ENERuY LATTICE

Q"NPO#$ FINAL FREE0NIT uETXYZ uRABIENT INITIAL
LATTICE NECBANIC NEXTARu 0CvNPRTXYZ
TNCu vERSI0N XTALLAT1

Q"NPOJP1 uRABIENT

Q"NPOJPD BESSIAN

Q"NPOJZ& LATTICE

Q"NPG'O B00NBS LATTICE N0LEC0LE

QRS&I#" ACTIvE B00NBS C0T0FFS BELETE FIELBFINAL
FREE0NIT uETXYZ INAuE INERTIA
INITIAL INSERT KAT0N LATTICE
NAKEREF NERuE N0LEC0LE PRTXYZ
RANB0N S0AK S0RT S0RT4
0NITCELL vERSI0N

QRS#$" FINAL FREE0NIT uETTEXT uETXYZ INITIAL
NAKEINT NEXTARu PRTINT REABINT
0PCASE vERSI0N

QRSGIV FIELB FINAL FREE0NIT uETXYZ INITIAL
KAT0N NAKEPBB N0LEC0LE PRTPBB
vERSI0N

QRS'#-#I }AC0BI R0TE0LER

QRS8RVRP B0NBS FINAL FREE0NIT uETXYZ INITIAL
PRTN0L2 vERSI0N

SN"JO FATAL
195 "#$%&' ()*+,) -./0* 195

SZNP(& NAKEXYZ TRINTEXT

196 "#$%&' ()*+,) -./0* 196
1D2 "*)4 ?;)*) M&H;C@B*)
This section contains biief uesciiptions of the sample calculations founu in the EXANPLE
subuiiectoiy of the TINKER uistiibution. These examples exeicise seveial of the cuiient TINKER
piogiams anu aie intenueu to pioviue a flavoi of the capabilities of the package.

N$#J$ &H;C@B*

Computes an estimation of the fiee eneigy of hyuiation of Cl
-
anion vs. Bi
-
anion via a 2 picoseconu
simulation on a ``hybiiu'' anion in a box of watei followeu by a fiee eneigy peituibation calculation

N'-J$ &H;C@B*

Peifoims an initial eneigy minimization on a peiiouic box containing 1Su aigon atoms followeu by 6
picoseconus of a moleculai uynamics using a mouifieu Beeman integiation algoiithm anu a
Beiseusen theimostat

?P(8"&' &H;C@B*

Peifoims a set of 1u uaussian uensity annealing (uBA) tiials on a clustei of 1S aigon atoms in an
attempt to locate the global minimum eneigy stiuctuie

?'NOV#$ &H;C@B*

ueneiates a TINKER file fiom a PBB file, followeu by a single point eneigy computation anu
ueteimination of the moleculai volume anu suiface aiea

?R?PJY&Q &H;C@B*

Fiist appioximately locates the tiansition state between chaii anu boat cyclohexane, followeu by
subsequent iefinement of the tiansition state anu a final vibiational analysis to show that a single
negative fiequency is associateu with the sauule point

I#NPN$#$& &H;C@B*

Finus all the local minima of alanine uipeptiue via a potential eneigy suiface scan using toisional
moues to jump between the minima

&$%&GYNP#$ &H;C@B*

Piouuces cooiuinates fiom the met-enkephalin amino aciu sequence anu phipsi angles, followeu by
tiuncateu Newton eneigy minimization anu ueteimination of the lowest fiequency noimal moue

>J'ONO#I& &H;C@B*

Conveits to a unit cell fiom fiactional cooiuinates, followeu by full ciystal eneigy minimization anu
ueteimination of optimal caibonyl oxygen eneigy paiameteis fiom a fit to lattice eneigy anu
stiuctuie

197 "#$%&' ()*+,) -./0* 197
Y&P#Q &H;C@B*

Peifoims a iigiu-bouy optimization of the packing of two iuealizeu polyalanine helices using only van
uei Waals inteiactions

8NP" &H;C@B*

Conveits a souium chloiiue assymetiic unit to the coiiesponuing unit cell, then iuns a ciystal
minimization staiting fiom the initial uiffiaction stiuctuie using Ewalu summation to mouel the
long-iange electiostatic inteiactions.

198 "#$%&' ()*+,) -./0* 198
1L2 V*367C;+m '*).B4)
The tables in this section pioviue CP0 benchmaiks foi basic TINKER eneigy anu ueiivative
evaluations, vibiational analysis anu moleculai uynamics. All times aie in seconus anu weie
measuieu with TINKER executables uimensioneu to maxatmof 1uuuu anu C;H7*)) of 1uuuuuu in
the souice file sizes.i. All calculations weie iun twice in iapiu succession on a quiet machine. The
times iepoiteu foi each benchmaik aie the iesults fiom the seconu iun. If you have built TINKER on
an alteinative machine type anu aie able to iun the benchmaiks on the auuitional machine type,
please senu the iesults foi inclusion in a futuie listing.

V&$?YON'% n1f ?;BC50.B/3 &3*+XE &^;B.;4/53

The system is an isolateu molecule of the 148-iesiuue piotein calmouulin with 2264 atoms using the
Ambei ff94 foice fielu. All inteiactions aie computeu with no use of cutoffs. Times listeu aie foi
calculation setup followeu by a single eneigy, eneigygiauient anu Bessian evaluation.

ON?Y#$&`J8`?JOG#P&' "RG& OY\ 8&"(G &$&'-R -'NI Y&88

Athlon XP 24uu+ (RB 8.u, Intel) 2uuu u.1S u.28 u.6u 2.96
Athlon XP 24uu+ (RB 8.u, PuI) 2uuu u.16 u.S1 u.7u S.6u
Athlon XP 24uu+ (RB 8.u, g77 S.2) 2uuu u.17 u.28 u.66 S.67
Athlon Thunueibiiu (RB 8.u, Intel) 14uu u.22 u.41 u.86 S.1S
Athlon Thunueibiiu (RB 8.u, PuI) 14uu u.21 u.44 1.uu S.92
Athlon Thunueibiiu (RB 8.u, g77 S.2) 14uu u.19 u.4u u.94 S.81
Athlon Classic (RB 8.u, Intel) 9Su u.Su u.64 1.42 7.u7
Athlon Classic (RB 8.u, PuI) 9Su u.Su u.69 1.6S 7.96
Athlon Classic (RB 8.u, g77 S.2) 9Su u.S1 u.6S 1.S7 7.94
Compaq Evo N61uc P4 (RB 8.u, Intel) 2uuu u.18 u.4S u.87 S.u8
Compaq Evo N61uc P4 (RB 8.u, PuI) 2uuu u.22 u.44 1.u6 4.27
Compaq Evo N61uc P4 (RB 8.u, Absoft) 2uuu u.17 u.S2 1.u6 S.9S
Compaq Evo N61uc P4 (RB 8.u, g77 S.2) 2uuu u.19 u.41 1.u7 4.41
Compaq Evo N61uc P4 (WinXP, CvF 6.6) 2uuu u.16 u.S8 u.98 S.S4
Compaq Evo N61uc P4 (WinXP, g77 S.2) 2uuu u.16 u.4u 1.u8 4.4S
Apple Powei Nac u4 (0SX 1u.2, Absoft) 7SS u.41 2.96 S.12 17.8S
Apple Powei Nac u4 (0SX 1u.2, g77 S.S) 7SS u.S7 1.98 S.79 14.48
Compaq AlphaSeivei BS1u (Tiu64 S.u) 466 u.SS 1.SS 1.9S 8.4u
SuI InuigoII R1uK (Iiix 6.S, NIPS) 19S 1.17 S.49 6.SS 2S.uS


V&$?YON'% nDf ?+;CA/3 ?+E)4;B &3*+XE &^;B.;4/53

The system is a unit cell of the 46-iesiuue piotein ciambin containing 2 polypeptiue chains, 2 ethanol
anu 178 watei molecules foi a total of 1S6u atoms using the 0PLS-0A foice fielu. Peiiouic bounuaiies
aie useu with paiticle mesh Ewalu foi electiostatics anu a 9.u - cutoff foi vuW inteiactions. Times
listeu aie foi calculation setup followeu by a single eneigy, eneigy giauient anu Bessian evaluation.

ON?Y#$&`J8`?JOG#P&' "RG& OY\ 8&"(G &$&'-R -'NI Y&88

Athlon XP 24uu+ (RB 8.u, Intel) 2uuu u.12 u.12 u.21 u.66
Athlon XP 24uu+ (RB 8.u, PuI) 2uuu u.1S u.14 u.24 u.6S
199 "#$%&' ()*+,) -./0* 199
Athlon XP 24uu+ (RB 8.u, g77 S.2) 2uuu u.14 u.1S u.28 u.81
Athlon Thunueibiiu (RB 8.u, Intel) 14uu u.19 u.17 u.Su u.91
Athlon Thunueibiiu (RB 8.u, PuI) 14uu u.18 u.18 u.S2 u.91
Athlon Thunueibiiu (RB 8.u, g77 S.2) 14uu u.17 u.17 u.S8 1.11
Athlon Classic (RB 8.u, Intel) 9Su u.26 u.2S u.47 1.46
Athlon Classic (RB 8.u, PuI) 9Su u.29 u.27 u.Su 1.42
Athlon Classic (RB 8.u, g77 S.2) 9Su u.27 u.27 u.S6 1.7u
Compaq Evo N61uc P4 (RB 8.u, Intel) 2uuu u.1S u.14 u.27 u.64
Compaq Evo N61uc P4 (RB 8.u, PuI) 2uuu u.22 u.19 u.SS u.88
Compaq Evo N61uc P4 (RB 8.u, Absoft) 2uuu u.14 u.22 u.S9 u.84
Compaq Evo N61uc P4 (RB 8.u, g77 S.2) 2uuu u.1S u.2u u.4S 1.1S
Compaq Evo N61uc P4 (WinXP, CvF 6.6) 2uuu u.14 u.17 u.SS u.8S
Compaq Evo N61uc P4 (WinXP, g77 S.2) 2uuu u.12 u.22 u.S2 1.16
Apple Powei Nac u4 (0SX 1u.2, Absoft) 7SS u.S2 u.S8 1.u9 S.11
Apple Powei Nac u4 (0SX 1u.2, g77 S.S) 7SS u.S1 u.42 u.79 2.S7
Compaq AlphaSeivei BS1u (Tiu64 S.u) 466 u.29 u.S8 u.64 1.9S
SuI InuigoII R1uK (Iiix 6.S, NIPS) 19S u.92 u.74 1.41 S.89


V&$?YON'% nLf G*@4/0* $5+C;B O50* ?;B6.B;4/53

The system is a minimum eneigy confoimation of a 2u-iesiuue peptiue containing one of each of the
stanuaiu amino acius foi a total of S28 atoms using the 0PLS-AA foice fielu without cutoffs. The time
iepoiteu is foi computation of the Bessian anu calculation of the noimal moues of the Bessian matiix
anu the vibiation fiequencies iequiiing two sepaiate matiix uiagonalization steps.

ON?Y#$&`J8`?JOG#P&' "RG& OY\ $J'ONP OJI&8

Athlon XP 24uu+ (RB 8.u, Intel) 2uuu 22
Athlon XP 24uu+ (RB 8.u, PuI) 2uuu 26
Athlon XP 24uu+ (RB 8.u, g77 S.2) 2uuu 24
Athlon Thunueibiiu (RB 8.u, Intel) 14uu S1
Athlon Thunueibiiu (RB 8.u, PuI) 14uu S4
Athlon Thunueibiiu (RB 8.u, g77 S.2) 14uu SS
Athlon Classic (RB 8.u, Intel) 9Su 46
Athlon Classic (RB 8.u, PuI) 9Su S1
Athlon Classic (RB 8.u, g77 S.2) 9Su 48
Compaq Evo N61uc P4 (RB 8.u, Intel) 2uuu 19
Compaq Evo N61uc P4 (RB 8.u, PuI) 2uuu 19
Compaq Evo N61uc P4 (RB 8.u, Absoft) 2uuu 2u
Compaq Evo N61uc P4 (RB 8.u, g77 S.2) 2uuu 19
Compaq Evo N61uc P4 (WinXP, CvF 6.6) 2uuu 19
Compaq Evo N61uc P4 (WinXP, g77 S.2) 2uuu 2u
Apple Powei Nac u4 (0SX 1u.2, Absoft) 7SS 67
Apple Powei Nac u4 (0SX 1u.2, g77 S.S) 7SS 62
Compaq AlphaSeivei BS1u (Tiu64 S.u) 466 S9
SuI InuigoII R1uK (Iiix 6.S, NIPS) 19S 144


V&$?YON'% nWf "#GLG <;4*+ V5H O5B*6.B;+ IE3;C/6)

200 "#$%&' ()*+,) -./0* 200
The system consists of 216 iigiu TIPSP watei molecules in a 18.64S - peiiouic box, 9.u - shifteu
eneigy switch cutoffs foi nonbonueu inteiactions. The time iepoiteu is foi 1uuu uynamics steps of
1.u fs each using the mouifieu Beeman integiatoi anu Rattle constiaints on all bonu lengths.

ON?Y#$&`J8`?JOG#P&' "RG& OY\ IR$NO#?8

Athlon XP 24uu+ (RB 8.u, Intel) 2uuu S7
Athlon XP 24uu+ (RB 8.u, PuI) 2uuu S4
Athlon XP 24uu+ (RB 8.u, g77 S.2) 2uuu 4S
Athlon Thunueibiiu (RB 8.u, Intel) 14uu S2
Athlon Thunueibiiu (RB 8.u, PuI) 14uu 47
Athlon Thunueibiiu (RB 8.u, g77 S.2) 14uu 6S
Athlon Classic (RB 8.u, Intel) 9Su 77
Athlon Classic (RB 8.u, PuI) 9Su 71
Athlon Classic (RB 8.u, g77 S.2) 9Su 96
Compaq Evo N61uc P4 (RB 8.u, Intel) 2uuu SS
Compaq Evo N61uc P4 (RB 8.u, PuI) 2uuu S4
Compaq Evo N61uc P4 (RB 8.u, Absoft) 2uuu SS
Compaq Evo N61uc P4 (RB 8.u, g77 S.2) 2uuu 91
Compaq Evo N61uc P4 (WinXP, CvF 6.6) 2uuu 6S
Compaq Evo N61uc P4 (WinXP, g77 S.2) 2uuu 94
Apple Powei Nac u4 (0SX 1u.2, Absoft) 7SS 2u9
Apple Powei Nac u4 (0SX 1u.2, g77 S.S) 7SS 17u
Compaq AlphaSeivei BS1u (Tiu64 S.u) 466 1u6
SuI InuigoII R1uK (Iiix 6.S, NIPS) 19S 28u


V&$?YON'% n[f "#$%&' <;4*+ V5H O5B*6.B;+ IE3;C/6)

The system consists of 216 AN0EBA flexible polaiizable atomic multipole watei molecules in a
18.64S - peiiouic box using iegulai Ewalu summation foi the electiostatics anu a 12.u - switcheu
cutoff foi vuW inteiactions. The time iepoiteu is foi 1uu uynamics steps of 1.u fs each using the
mouifieu Beeman integiatoi anu u.u1 Bebye ims conveigence foi inuuceu uipole moments.

ON?Y#$&`J8`?JOG#P&' "RG& OY\ IR$NO#?8

Athlon XP 24uu+ (RB 8.u, Intel) 2uuu 1u8
Athlon XP 24uu+ (RB 8.u, PuI) 2uuu 1u4
Athlon XP 24uu+ (RB 8.u, g77 S.2) 2uuu 128
Athlon Thunueibiiu (RB 8.u, Intel) 14uu 16S
Athlon Thunueibiiu (RB 8.u, PuI) 14uu 1S8
Athlon Thunueibiiu (RB 8.u, g77 S.2) 14uu 18S
Athlon Classic (RB 8.u, Intel) 9Su 282
Athlon Classic (RB 8.u, PuI) 9Su 261
Athlon Classic (RB 8.u, g77 S.2) 9Su Su7
Compaq Evo N61uc P4 (RB 8.u, Intel) 2uuu 1S6
Compaq Evo N61uc P4 (RB 8.u, PuI) 2uuu 191
Compaq Evo N61uc P4 (RB 8.u, Absoft) 2uuu 226
Compaq Evo N61uc P4 (RB 8.u, g77 S.2) 2uuu 24S
Compaq Evo N61uc P4 (WinXP, CvF 6.6) 2uuu 176
Compaq Evo N61uc P4 (WinXP, g77 S.2) 2uuu 26S
Apple Powei Nac u4 (0SX 1u.2, Absoft) 7SS 68u
201 "#$%&' ()*+,) -./0* 201
Apple Powei Nac u4 (0SX 1u.2, g77 S.S) 7SS 479
Compaq AlphaSeivei BS1u (Tiu64 S.u) 466 SS8
SuI InuigoII R1uK (Iiix 6.S, NIPS) 19S 868

202 "#$%&' ()*+,) -./0* 202
1W2 ?5BB;A5+;45+) MN6m35:B*0XC*34)
The TINKER package has uevelopeu ovei a peiiou of many yeais, veiy slowly uuiing the late-198us,
anu moie iapiuly since the miu-199us in }ay Ponuei's ieseaich gioup at the Washington 0niveisity
School of Neuicine in Saint Louis. Nany people have playeu significant ioles in the uevelopment of
the package into its cuiient foim. The majoi contiibutois aie listeu below:

84*:'.A*3)4*/3 cooiuinate inteiconveisions; oiiginal optimization methous
anu toisional angle manipulation

?+;/X %.30+54 moleculai suiface aiea & volume anu theii ueiivatives

87;:3 Y.)453 oiiginal ANBER0PLS implementation; fiee eneigy
calculations; time coiielation functions

O/m* I.0*m initial multipole mouels foi peptiues anu pioteins

R53X FO/m*F %53X multipole electiostatics; uipole polaiization; ieaction fielu
tieatment; TINKER watei mouel

'**6* Y;+4 potential smoothing methouology; Scheiaga's BEN,
Stiaub's uBA anu extensions

O/m* Y50)053 extension of the TINKER uistgeom piogiam anu its
application to NNR N0E stiuctuie ueteimination

'57/4 G;@@. potential smoothing methouology anu PSS algoiithms;
iigiu bouy optimization; uBSA solvation ueiivatives

</j3;30 O55/j NNS uiiectional hyuiogen bonuing teim; ciystal lattice
minimization coue

-*+;B0 P5*99B*+ stochasticLangevin uynamics implementation

O;+/3; Z5+5A/*^; nucleic aciu builuing mouule anu paiametei tianslation
$/3; 85m5B5^;

G*4*+ V;X5))/ AN0EBA foice fielu paiameteis foi alkanes anu uiatomics

G*3XE. '*3 Ewalu summation foi polaiizable atomic multipoles;
AN0EBA foice fielu foi watei, oiganics anu peptiues

N30*+) ?;+B))53 oiiginal liganu fielu potential eneigy teim foi tiansition metals

N30+*E %.4*@5^ integiatoi foi iigiu-bouy uynamics tiajectoiies

"5C I;+0*3 Paiticle Nesh Ewalu (PNE) coue, anu uevelopment of PNE
foi the AN0EBA foice fielu

203 "#$%&' ()*+,) -./0* 203
NB;3 -+5))9/*B0 Nonte Cailo minimization; tophat potential smoothing

O/67;*B 8673/*0*+) Foice Fielu Exploiei u0I foi TINKER; neighboi lists foi
nonbonueu inteiactions

?7.;3j/* <. solvation fiee eneigy calculations; AN0EBA nucleic aciu foice
fielu; paiameteiization tools foi TINKER
e.)4/3 Q/;3X angulai oveilap anu valence bonu potential mouels foi
tiansition metals
I;^/0 -57;+; 0penNP paiallelization of eneigy teims incluuing PNE,
anu paiallel neighboi lists

It is ciitically impoitant that TINKER's uistiibuteu foice fielu paiametei sets exactly iepiouuce the
intent of the oiiginal foice fielu authois. We woulu like to thank e.B/;3 "/+;05`'/^*) (0PLS-AA),
NB*H O;6%*+*BB (CBARNN27), </B9+*0 ^;3 -.3)4*+*3 (uR0N0S), anu N0+/;3 '5/4A*+X anu
?;+B5) 8/CC*+B/3X (ANBER) foi theii help in testing TINKER's iesults against those given by the
authentic piogiams anu paiametei sets. P5. NBB/3X*+ pioviueu upuateu paiameteis foi NN2 anu
NNS on seveial occasions. Bis veiy successful methous pioviueu the oiiginal inspiiation foi the
uevelopment of TINKER.

Still othei woikeis have uevoteu consiueiable time in ueveloping coue that will hopefully be
incoipoiateu into futuie TINKER veisions; foi example, e/C %+*)) (0FF implementation) anu
O/67;*B 87**4) (numeious coue optimizations, theimouynamic integiation). Finally, we wish to
thank the many useis of the TINKER package foi theii suggestions anu comments, piaise anu
ciiticism, which have iesulteu in a vaiiety of impiovements.

204 "#$%&' ()*+,) -./0* 204
1[2 '*9*+*36*) M8.XX*)4*0 '*;0/3X
This section contains a list of the iefeiences to geneial theoiy, algoiithms anu implementation uetails
which have been of use uuiing the uevelopment of the TINKER package. Nethous uesciibeu in some
of the iefeiences have been implementeu in uetail within the TINKER souice coue. 0thei iefeiences
contain useful backgiounu infoimation although the algoiithms themselves aie now obsolete. Still
othei papeis contain iueas oi extensions planneu foi futuie inclusion in TINKER. Refeiences foi
specific foice fielu paiametei sets aie pioviueu in an eailiei section of this 0sei's uuiue. This list is
heavily skeweu towaiu biomolecules in geneial anu pioteins in paiticulai. This bias ieflects oui
gioup's majoi inteiests; howevei an attempt has been maue to incluue methous which shoulu be
geneially applicable.

GN'"#NP P#8" J> OJP&?(PN' O&?YN$#?8 8J>"<N'& GN?%N-&8

ANBER Petei Kollman, 0niveisity of Califoinia, San Fiancisco
ANNP Rob Baiiison, Thomas }effeison 0niveisity, Philauelphia
ARu0S Anuy NcCammon, 0niveisity of Califoinia, San Biego
B0SS William }oigensen, Yale 0niveisity
BR0uEL Shoshona Wouak, Fiee 0niveisity of Biussels
CFF Shneioi Lifson, Weizmann Institute
CBARNN Naitin Kaiplus, Baivaiu 0niveisity
CBARNNuENN Beinaiu Biooks, National Institutes of Bealth, Bethesua
BELPBI Bastian van ue uiaaf, Belft 0niveisity of Technology
BISC0vER Noleculai Simulations Inc., San Biego
BL_P0LY W. Smith & T. Foiestei, CCPS, Baiesbuiy Laboiatoiy
ECEPP Baiolu Scheiaga, Coinell 0niveisity
ENCAB Nichael Levitt, Stanfoiu 0niveisity
FANT0N Weinei Biaun, 0niveisity of Texas, ualveston
FEBER2 Nobuhiio uo, Kyoto 0niveisity
uR0NACS Beiman Beienusen, 0niveisity of uioningen
uR0N0S Wilfieu van uunsteien, BI0N0S anu ETB, Zuiich
INPACT Ronalu Levy, Rutgeis 0niveisity
NACR0N0BEL Schouingei, Inc., }eisey City, New }eisey
NN2NNSNN4 N. Lou Allingei, 0niveisity of ueoigia
NNC Cliff Bykstia, Inuiana 0niv.=Puiuue 0niv. at Inuianapolis
NNFF Tom Balgien, Neick Reseaich Laboiatoiies, Rahway
NNTK Koniau Binsen, Inst. of Stiuctuial Biology, uienoble
N0IL Ron Elbei, Coinell 0niveisity
N0LARIS Aiieh Waishal, 0niveisity of Southein Califoinia
N0LBY Keith Refson, 0xfoiu 0niveisity
N0SCIT0 Bietmai Paschek & Alfons ueigei, 0niveisit%t Boitmunu
NANB Klaus Schulten, 0niveisity of Illinois, 0ibana
00NPAA Anuy NcCammon, 0niveisity of Califoinia, San Biego
0RAL Kaiel Zimmeiman, INRA, }ouy-en-}osas, Fiance
0RIENT Anthony Stone, Cambiiuge 0niveisity
PCN0BEL Kevin uilbeit, Seiena Softwaie, Bloomington, Inuiana
PEFF }an Billen, 0niveisity of Pietoiia, South Afiica
Q }ohan -qvist, 0ppsala 0niveisity
SIBFA Nohau uiesh, INSERN, CNRS, Paiis
SIuNA }an Beimans, 0niveisity of Noith Caiolina
SPASIBA ueiaiu veigoten, 0niveisitE ue Lille
SPASNS Baviu Spellmeyei anu the Kollman uioup, 0CSF
205 "#$%&' ()*+,) -./0* 205
TINKER }ay Ponuei, Washington 0niveisity, St. Louis
XPL0RCNS Axel Bingei, Stanfoiu 0niveisity
YANNP Stephen Baivey, 0niveisity of Alabama, Biimingham
YASP Floiian Nuellei-Plathe, ETB Zentium, Zuiich
YETI Angelo veuani, Biogiafik-Laboi SR, Basel

NOV&' B. A Peailman, B. A. Case, }. W. Caluwell, W. S. Ross, T. E. Cheatham III, S. BeBolt, B.
Feiguson, u. Seibel anu P. Kollman, ANBER, a Package of Computei Piogiams foi Applying Noleculai
Nechanics, Noimal Noue Analysis, Noleculai Bynamics anu Fiee Eneigy Calculations to Simulate the
Stiuctuial anu Eneigetic Piopeities of Nolecules, C)D4A E-0"A C)DD95A, D>, 1-41 (199S)

N'-J8 T. P. Stiaatsma anu }. A. NcCammon, ARu0S, a vectoiizeu ueneial Noleculai Bynamics
Piogiam, BA C)D49*A C-+DA, >>, 94S-9S1 (199u)

?YN'OO B. R. Biooks, R. E. Biuccoleii, B. B. 0lafson, B. }. States, S. Swaminathan anu N. Kaiplus,
CBARNN: A Piogiam foi Naciomoleculai Eneigy, Ninimization, anu Bynamics Calculations, BA
C)D49*A C-+DA, E, 187-217 (198S)

&$?NI N. Levitt, N. Biishbeig, R. Shaion anu v. Baggett, Potential Eneigy Function anu
Paiameteis foi Simulations foi the Noleculai Bynamics of Pioteins anu Nucleic Acius in Solution,
C)D4A E-0"A C)DD95A, D>, 21S-2S1 (199S)

>N$"JO T. Schaumann, W. Biaun anu K. Wuitiich, The Piogiam FANT0N foi Eneigy Refinement
of Polypeptiues anu Pioteins 0sing a Newton-Raphson Ninimizei in Toision Angle Space,
F.)4)I0D+2", <D, 679-694 (199u)

>&I&'cD B. Wako, S. Enuo, K. Nagayama anu N. uo, FEBER2: Piogiam foi Static anu Bynamic
Confoimational Eneigy Analysis of Nacio-molecules in Biheuial Angle Space, C)D4A E-0"A C)DD95A,
D>, 2SS-2S1 (199S)

-'JON?8 E. Linuahl, B. Bess anu B. van uei Spoel, uR0NACS S.u: A Package foi Noleculai
Simulation anu Tiajectoiy Analysis, BA K)IA K)IA, @, Su6-S17 (2uu1)

-'JOJ8 W. R. P. Scott, P. B. Bunenbeigei , I. u. Tiioni, A. E. Naik, S. R. Billetei, }. Fennen, A. E.
Toiua, T. Bubei, P. Kiugei, W. F. van uunsteien, The uR0N0S Biomoleculai Simulation Piogiam
Package, BA E-0"A C-+DA G, >?=, SS96-S6u7 (1999)

#OGN?" B. B. Kitchen, F. Biiata, }. B. Westbiook, R. Levy, B. Kofke anu N. Yaimush, Conseiving
Eneigy uuiing Noleculai Bynamics Simulations of Watei, Pioteins, anu Pioteins in Watei, BA C)D49*A
C-+DA, >?, 1169-118u (199u)

ON?'JOJI&P F. Nahamaui, N. u. }. Richaius, W. C. uuiua, R. Liskamp, N. Lipton, C. Caufielu, u.
Chang, T. Benuiickson anu W. C. Still, NacioNouel=An Integiateu Softwaie System foi Noueling
0iganic anu Biooiganic Nolecules 0sing Noleculai Nechanics, BA C)D49*A C-+DA, >>, 44u-467 (199u)

OOD N. L. Allingei, Confoimational Analysis. 1Su. NN2. A Byuiocaibon Foice Fielu 0tilizing v
1
anu v
2
Toisional Teims, BA GDA C-+DA H)6A, DD, 8127-81S4 (1977)

OOL N. L. Allingei, Y. B. Yuh anu }.-B. Lii, Noleculai Nechanics. The NNS Foice Fielu foi
Byuiocaibons, BA GDA C-+DA H)6A, >>>, 8SS1-8S66 (1989)
206 "#$%&' ()*+,) -./0* 206

OOW N. L. Allingei, K. Chen anu }.-B. Lii, An Impioveu Foice Fielu (NN4) foi Satuiateu
Byuiocaibons, BA C)D49*A C-+DA, >@, 642-668 (1996)

OO? C. E. Bykstia, Noleculai Nechanics foi Weakly Inteiacting Assemblies of Raie uas Atoms anu
Small Nolecules, BA GDA C-+DA H)6A, >>>, 6168-6174 (1989)

OO>> T. A. Balgien, Neick Noleculai Foice Fielu. I. Basis, Foim, Scope, Paiameteiization, anu
Peifoimance of NNFF94, BA C)D49*A C-+DA, >@, 49u-S16 (1996)

OJ#P R. Elbei, A. Roitbeig, C. Simmeiling, R. uolustein, B. Li, u. veikhivei, C. Keasai, }. Zhang anu A.
0litsky, N0IL: A Piogiam foi Simulations of Naciomolecules, C)D4A E-0"A C)DD95A, D>, 1S9-189
(199S)

OJ8?#"J See the web site at http:gantei.chemie.uni-uoitmunu.ue~pasmoscito.html

$NOI L. KalE, R. Skeel, N. Bhanuaikai, R. Biunnei, A. uuisoy, N. Kiawetz, }. Phillips, A. Shinozaki,
K. vaiauaiajan anu K. Schulten, NANB2: uieatei Scalability foi Paiallel Noleculai Bynamics, BA
C)D49*A E-0"A, >A>, 28S-S12 (1999)

JJOGNN u. A. Bubei anu }. A. NcCammon, 00NPAA=0bject-oiienteu Nouel foi Piobing
Assemblages of Atoms, BA C)D49*A E-0"A, >A>, 264-282 (1999)

J'NP K. Zimmeimann, 0RAL: All Puipose Noleculai Nechanics Simulatoi anu Eneigy Ninimizei, BA
C)D49*A C-+DA, ><, S1u-S19 (1991)

G?OJI&P See the web site at http:www.seienasoft.com

G&>> }. L. N. Billen, PEFF: A Piogiam foi the Bevelopment of Empiiical Foice Fielus, BA C)D49*A
C-+DA, >=, 2S7-267 (1992)

K See the web site at http:aqvist.bmc.uu.seQ

8#V>N N. uiesh, Intei- anu Intiamoleculai Inteiactions. Inception anu Refinements of the SIBFA,
Noleculai Nechanics (SNN) Pioceuuie, a Sepaiable, Polaiizable Nethouology uiounueu on (F G.&"&4
SCFNP2 Computations. Examples of Applications to Noleculai Recognition Pioblems, BA C-.DA E-0"A
ECF, DE, 1S6S-1416 (1997)

8#-ON See the web site at http:femto.meu.unc.euuSIuNA

8GN8#VN P. Beiieumaux anu u. veigoten, A New Spectioscopic Noleculai Nechanics Foice-Fielu -
Paiameteis Foi Pioteins, BA C-+DA E-0"A, >?<, 8S86-86uS (199S)

"#$%&' See the web site at http:uashei.wustl.euutinkei

RNOOG R. K.-Z. Tan anu S. C. Baivey, Yammp: Bevelopment of a Noleculai Nechanics Piogiam
0sing the Nouulai Piogiamming Nethou, BA C)D49*A C-+DA, >E, 4SS-47u (199S)

R&"# A. veuani, YETI: An Inteiactive Noleculai Nechanics Piogiam foi Small-Nolecule Piotein
Complexes, BA C)D49*A C-+DA, D, 269-28u (1988)
207 "#$%&' ()*+,) -./0* 207

OJP&?(PN' O&?YN$#?8

0. Buikeit anu N. L. Allingei, O5B*6.B;+ O*67;3/6), Ameiican Chemical Society, Washington, B.C.,
1982

P. Comba anu T. W. Bambley, O5B*6.B;+ O50*B/3X 59 #35+X;3/6 ?5C@5.30)U D30 &02, Wiley-vCB,
New Yoik, 2uu1

K. Nachiua, G+/36/@B*) 59 O5B*6.B;+ O*67;3/6), Kouansha}ohn Wiley & Sons, TokyoNew Yoik,
1999

A. K. RappE anu C. }. Casewit, O5B*6.B;+ O*67;3/6) ;6+5)) ?7*C/)4+E, 0niveisity Science Books,
Sausalito, CA, 1997

K. Rasmussen, G54*34/;B &3*+XE >.364/53) /3 ?5395+C;4/53;B N3;BE)/) (Lectuie Notes in
Chemistiy, vol. 27), Spiingei-veilag, Beilin, 198S

?JOG("&' 8#O(PN"#J$ O&"YJI8

N. P. Allen anu B. }. Tiluesley, ?5C@.4*+ 8/C.B;4/53 59 P/d./0), 0xfoiu 0niveisity Piess, 0xfoiu,
1987

C. }. Ciamei, &))*34/;B) 59 ?5C@.4;4/53;B ?7*C/)4+Ef "7*5+/*) ;30 O50*B), }ohn Wiley anu Sons,
New Yoik, 2uu2

N. }. Fielu, N G+;64/6;B #34+50.64/53 45 47* 8/C.B;4/53 59 O5B*6.B;+ 8E)4*C), Cambiiuge 0niv.
Piess, Cambiiuge, 1999

B. Fiankel anu B. Smit, (30*+)4;30/3X O5B*6.B;+ 8/C.B;4/53f >+5C NBX5+/47C) 45 N@@B/6;4/53)U
D30 &02, Acauemic Piess, San Biego, CA, 2uu1

}. N. Baile, O5B*6.B;+ IE3;C/6) 8/C.B;4/53f &B*C*34;+E O*4750), }ohn Wiley anu Sons, New Yoik,
1992

F. }ensen, #34+50.64/53 45 ?5C@.4;4/53;B ?7*C/)4+E, }ohn Wiley anu Sons, New Yoik, 1998

A. R. Leach, O5B*6.B;+ O50*BB/3Xf G+/36/@B*) ;30 N@@B/6;4/53)U D30 &02, Auuison Wesley Longman,
Essex, Englanu, 2uu1

B. C. Rapapoit, "7* N+4 59 O5B*6.B;+ IE3;C/6) 8/C.B;4/53U D30 &02, Cambiiuge 0niveisity Piess,
Cambiiuge, 2uu4

T. Schlick, O5B*6.B;+ O50*B/3X ;30 8/C.B;4/53, Spiingei-veilag, New Yoik, 2uu2

OJI&P#$- J> V#JPJ-#?NP ON?'JOJP&?(P&8

0. N. Beckei, A. B. NacKeiell, }i., B. Roux anu N. Watanabe, Eus., ?5C@.4;4/53;B V/567*C/)4+E ;30
V/5@7E)/6)U Naicel Bekkei, New Yoik, 2uu1

208 "#$%&' ()*+,) -./0* 208
C. L. Biooks III, N. Kaiplus anu B. N. Pettitt, G+54*/3)f N "7*5+*4/6;B G*+)@*64/^* 59 IE3;C/6)U
84+.64.+*U ;30 "7*+C50E3;C/6), }ohn Wiley anu Sons, New Yoik, 1988

v. Baggett, Eu., G+54*/3 8/C.B;4/53) kN0^;36*) /3 G+54*/3 ?7*C/)4+EU Z5B2 ]]l, Acauemic
PiessElseviei, New Yoik, 2uuS

}. A. NcCammon anu S. Baivey, IE3;C/6) 59 G+54*/3) ;30 $.6B*/6 N6/0), Cambiiuge 0niveisity
Piess, Cambiiuge, 1987

W. F. van uunsteien, P. K. Weinei anu A. }. Wilkinson, ?5C@.4*+ 8/C.B;4/53 59 V/5C5B*6.B;+
8E)4*C)U Z5B2 1`L, Kluwei Acauemic Publisheis, Boiuiecht, 1989-1997

?J$e(-N"& -'NI#&$" N$I K(N8#`$&<"J$ JG"#O#SN"#J$

}. Noceual anu S. }. Wiight, $.C*+/6;B J@4/C/\;4/53, Spiingei-veilag, New Yoik, 1999

S. u. Nash anu A. Sofei, P/3*;+ ;30 $53B/3*;+ G+5X+;CC/3X, Ncuiaw-Bill, New Yoik, 1996

R. Fletchei, G+;64/6;B O*4750) 59 J@4/C/\;4/53, }ohn Wiley & Sons Ltu., Chichestei, 1987

B. u. Luenbeigei, P/3*;+ ;30 $53B/3*;+ G+5X+;CC/3X, 2nu Eu., Auuison-Wesley, Reauing, NA,
1984

P. E. uill, W. Nuiiay anu N. B. Wiight, G+;64/6;B J@4/C/\;4/53, Acauemic Piess, New Yoik, 1981

}. Noceual, 0puating Quasi-Newton Natiices with Limiteu Stoiage, K:*-A C)D4A, 77S-782 (198u)

S. }. Watowich, E. S. Neyei, R. Bagstiom anu R. }osephs, A Stable, Rapiuly Conveiging Conjugate
uiauient Nethou foi Eneigy Ninimization, BA C)D49*A C-+DA, D, 6Su-661 (1988)

W. C. Baviuon, 0ptimally Conuitioneu 0ptimization Algoiithms without Line Seaiches, K:*-A E2)MA, D,
1-Su (197S)

"'($?N"&I $&<"J$ JG"#O#SN"#J$

}. W. Ponuei anu F. N. Richaius, An Efficient Newton-like Nethou foi Noleculai Nechanics Eneigy
Ninimization of Laige Nolecules, BA C)D49*A C-+DA, H, 1u16-1u24 (1987)

R. S. Bembo anu T. Steihaug, Tiuncateu-Newton Algoiithms foi Laige-Scale 0nconstiaineu
0ptimization, K:*-A E2)MA, <B, 19u-212 (198S)

S. C. Eisenstat anu B. F. Walkei, Choosing the Foicing Teims in an Inexact Newton Nethou, H=GK BA
H6.A C)D49*A, >@, 16-S2 (1996)

T. Schlick anu N. 0veiton, A Poweiful Tiuncateu Newton Nethou foi Potential Eneigy Ninimization,
BA C)D49*A C-+DA, H, 1u2S-1uS9 (1987)

B. S. Keishaw, The Incomplete Cholesky-Conjugate uiauient Nethou foi the Iteiative Solution of
Systems of Lineai Equations, BA C)D49*A E-0"A, <B, 4S-6S (1978)

209 "#$%&' ()*+,) -./0* 209
T. A. Nanteuffel, An Incomplete Factoiization Technique foi Positive Befinite Lineai Systems, K:*-A
C)D4A, =E, 47S-497 (198u)

P. Beiieumaux, u. Zhang anu T. Schlick anu B. R. Biooks, A Tiuncateu Newton Ninimizei Auapteu foi
CBARNN anu Biomoleculai Applications, BA C)D49*A C-+DA, >A, SS2-SS2 (1994)

I. S. Buff, A. N. Eiisman anu }. K. Reiu, I/+*64 O*4750) 95+ 8@;+)* O;4+/6*), 0xfoiu 0niveisity Piess,
0xfoiu, 1986

GJ"&$"#NP &$&'-R 8OJJ"Y#$-

R. v. Pappu, R. K. Bait anu }. W. Ponuei, Analysis anu Application of Potential Eneigy Smoothing
Nethous foi ulobal 0ptimization, BA E-0"A C-+DA F, >?<, 972S-9742 (1998)

L. Piela, }. Kostiowicki anu B. A. Scheiaga, The Nultiple-Ninima Pioblem in the Confoimational
Analysis of Nolecules. Befoimation of the Potential Eneigy Bypeisuiface by the Biffusion Equation
Nethou, BA E-0"A C-+DA, D=, SSS9-SS46 (1989)

}. Na anu }. E. Stiaub, Simulateu Annealing 0sing the Classical Bensity Bistiibution, BA C-+DA E-0"A,
>?>, SSS-S41 (1994)

C. Tsoo anu C. L. Biooks, Clustei Stiuctuie Beteimination 0sing uaussian Bensity Bistiibution ulobal
Ninimization Nethous, BA C-+DA E-0"A, >?>, 64uS-6411 (1994)

S. Nakamuia, B. Biiose, N. Ikeguchi anu }. Boi, Confoimational Eneigy Ninimization 0sing a Two-
Stage Nethou, BA E-0"A C-+DA, DD, 8S74-8S78 (199S)

T. Bubei, A. E. Toiua anu W. F. van uunsteien, Stiuctuie 0ptimization Combining Soft-Coie
Inteiaction Functions, the Biffusion Equation Nethou, anu Noleculai Bynamics, BA E-0"A C-+DA G, >?>,
S926-S9Su (1997)

S. Schelstiaete anu B. veischelue, Finuing Ninimum-Eneigy Configuiations of Lennaiu-}ones
Clusteis 0sing an Effective Potential, BA E-0"A C-+DA G, >?>, S1u-S1S (1998)

I. Anuiicioaei anu }. E. Stiaub, ulobal 0ptimization 0sing Bau Beiivatives: Beiivative-Fiee Nethou foi
Noleculai Eneigy Ninimization, BA C)D49*A C-+DA, >D, 144S-14SS (1998)

L. Piela, Seaich foi the Nost Stable Stiuctuies on Potential Eneigy Suifaces, C)IIA CP+6-A C-+DA
C)DD95A, B=, 1S68-1S8u (1998)

oo8$#>>&',, -PJVNP JG"#O#SN"#J$

A. 0. uiiewank, ueneializeu Bescent foi ulobal 0ptimization, BA L4*A <-+)2A G44IA, =E, 11-S9 (1981)

R. A. R. Butlei anu E. E. Slaminka, An Evaluation of the Sniffei ulobal 0ptimization Algoiithm 0sing
Stanuaiu Test Functions, BA C)D49*A E-0"A, DD, 28-S2 (199S)

}. W. Rogeis anu R. A. Bonnelly, Potential Tiansfoimation Nethous foi Laige-Scale ulobal
0ptimization, H=GK BA L4*.DA, A, 871-891 (199S)

210 "#$%&' ()*+,) -./0* 210
#$"&-'N"#J$ O&"YJI8 >J' OJP&?(PN' IR$NO#?8

B. Beeman, Some Nultistep Nethous foi 0se in Noleculai Bynamics Calculations, BA C)D49*A E-0"A,
<?, 1Su-1S9 (1976)

N. Levitt anu B. Neiiovitch, Integiating the Equations of Notion, BA K)IA F.)IA, >BH, 617-62u (198S)

}. Aqvist, W. F. van uunsteien, N. Leijonmaick anu 0. Tapia, A Noleculai Bynamics Stuuy of the C-
Teiminal Fiagment of the L7L12 Ribosomal Piotein, BA K)IA F.)IA, >H=, 461-477 (198S)

W. C. Swope, B. C. Anueisen, P. B. Beiens anu K. R. Wilson, A Computei Simulation Nethou foi the
Calculation of Equilibiium Constants foi the Foimation of Physical Clusteis of Nolecules: Application
to Small Watei Clusteis, BA C-+DA E-0"A, @B, 6S7-649 (1982)

?J$8"'N#$" IR$NO#?8

W. F. van uunsteien anu B. }. C. Beienusen, Algoiithms foi Naciomoleculai Bynamics anu Constiaint
Bynamics, K)IA E-0"A, =E, 1S11-1S27 (1977)

u. Ciccotti, N. Feiiaiio anu }.-P. Ryckaeit, Noleculai Bynamics of Rigiu Systems in Caitesian
Cooiuinates: A ueneial Foimulation, K)IA E-0"A, E@, 12SS-1264 (1982)

B. C. Anueisen, Rattle: A ``velocity'' veision of the Shake Algoiithm foi Noleculai Bynamics
Calculations, BA C)D49*A E-0"A, A<, 24-S4 (198S)

R. Kutteh, RATTLE Recipe foi ueneial Bolonomic Constiaints: Angle anu Toision Constiaints, CCE$
(+1"I+**+2, EB, 9-17 (1998) |available fiom the web site at
http:www.ul.ac.ukCCPCCPSnewslettei_inuex.htmlj

B. }. Palmei, Biiect Application of SBAKE to the velocity veilet Algoiithm, BA C)D49*A E-0"A, >?E, 47u-
472 (199S)

S. Niyamoto anu P. A. Kollman, SETTLE: An Analytical veision of the SBAKE anu RATTLE Algoiithm
foi Rigiu Watei Nouels, BA C)D49*A C-+DA, >=, 9S2-962 (1992)

B. Bess, B. Bekkei, B. }. C. Beienusen anu }. u. E. N. Fiaaije, LINCS: A Lineai Constiaint Solvei foi
Noleculai Simulations, BA C)D49*A C-+DA, >H, 146S-1472 (1997)

}. T. Slushei anu P. T. Cummings, Non-Iteiative Constiaint Bynamics using velocity-Explicit veilet
Nethous, K)IA H.D9IA, >H, 21S-224 (1996)

PN$-&Z#$U V'J<$#N$ N$I 8"J?YN8"#? IR$NO#?8

N. P. Allen, Biownian Bynamics Simulation of a Chemical Reaction in Solution, K)IA E-0"A, E?, 1u7S-
1u87 (198u)

W. F. van uunsteien anu B. }. C. Beienusen, Algoiithms foi Biownian Bynamics, K)IA E-0"A, EA, 6S7-
647 (1982)

211 "#$%&' ()*+,) -./0* 211
F. uuainieii anu W. C. Still, A Rapiuly Conveigent Simulation Nethou: Nixeu Nonte CailoStochastic
Bynamics, BA C)D49*A C-+DA, >A, 1Su2-1S1u (1994)

N. u. Pateilini anu B. N. Feiguson, Constant Tempeiatuie Simulations using the Langevin Equation
with velocity veilet Integiation, C-+DA E-0"A, <=B, 24S-2S2 (1998)

?J$8"N$" "&OG&'N"('& N$I G'&88('& IR$NO#?8

B. }. C. Beienusen, }. P. N. Postma, W. F. van uunsteien, A. BiNola anu }. R. Baak, Noleculai Bynamics
with Coupling to an Exteinal Bath, BA C-+DA E-0"A, H>, S684-S69u (1984)

W. u. Boovei, Canonical Bynamics: Equilibiium Phase-space Bistiibutions, E-0"A @+!A G, =>, 169S-
1697 (198S)

}. }. Noiales, S. Toxvaeiu anu L. F. Rull, Computei Simulation of a Phase Tiansition at Constant
Tempeiatuie anu Piessuie, E-0"A @+!A G, =E, 149S-1498 (1986)

B. R. Biooks, Algoiithms foi Noleculai Bynamics at Constant Tempeiatuie anu Piessuie, Inteinal
Repoit of Bivision of Computei Reseaich anu Technology, National Institutes of Bealth, 1988.

N. Levitt, Noleculai Bynamics of Native Piotein: Computei Simulation of Tiajectoiies, BA K)IA F.)IA,
>BH, S9S-62u (198S)

J("`J>`GPN$& I&>J'ON"#J$ "&'O8

}. R. Naple, 0. Binai anu A. T. Baglei, Beiivation of Foice Fielus foi Noleculai Nechanics anu
Bynamics fiom (F &.&"&4 Eneigy Suifaces, E2)6A (:*IA G6:3A H6.A QHG, HA, SSSu-SSS4 (1988)

S.-B. Lee, K. Palmo anu S. Kiimm, New 0ut-of-Plane Angle anu Bonu Angle Inteinal Cooiuinates anu
Relateu Potential Eneigy Functions foi Noleculai Nechanics anu Bynamics Simulations, BA C)D49*A
C-+DA, <?, 1u67-1u84 (1999)

N$NPR"#?NP I&'#ZN"#Z&8 J> GJ"&$"#NP >($?"#J$8

K. }. Nillei, R. }. Binue anu }. Anueison, Fiist anu Seconu Beiivative Natiix Elements foi the
Stietching, Benuing, anu Toisional Eneigy, BA C)D49*A C-+DA, >?, 6S-76 (1989)

B. B. Fabei anu C. Altona, 0TABS: A veisatile Piogiamme Package foi the Calculation of Noleculai
Piopeities by Foice Fielu Nethous, C)D49*+2" R C-+D."*20, >, 2uS-21S (1977)

W. C. Swope anu B. N. Feiguson, Alteinative Expiessions foi Eneigies anu Foices Bue to Angle
Benuing anu Toisional Eneigy, Repoit uS2u-SS61, BA C)D49*A C-+DA, >=, S8S-S94 (1992)

A. Blonuel anu N. Kaiplus, New Foimulation foi Beiivatives of Toision Angles anu Impiopei Toision
Angles in Noleculai Nechanics: Elimination of Singulaiities, BA C)D49*A C-+DA, >@, 11S2-1141 (1996)

R. E. Tuzun, B. W. Noiu anu B. u. Sumptei, Efficient Tieatment of 0ut-of-Plane Benu anu Impiopei
Toision Inteiactions in NN2, NNS, anu NN4 Noleculai Nechanics Calculations, BA C)D49*A C-+DA,
>H, 18u4-1811 (1997)

212 "#$%&' ()*+,) -./0* 212
"J'8#J$NP 8GN?& I&'#ZN"#Z&8 N$I $J'ONP OJI&8

N. Levitt, C. Sanuei anu P. S. Stein, Piotein Noimal-moue Bynamics: Tiypsin Inhibitoi, Ciambin,
Ribonuclease anu Lysozyme, BA K)IA F.)IA, >H>, 42S-447 (198S)

N. Levitt, Piotein Foluing by Restiaineu Eneigy Ninimization anu Noleculai Bynamics, BA K)IA F.)IA,
>@?, 72S-764 (198S)

B. Wako anu N. uo, Algoiithm foi Rapiu Calculation of Bessian of Confoimational Eneigy Function of
Pioteins by Supeicomputei, BA C)D49*A C-+DA, H, 62S-6SS (1987)

B. Abe, W. Biaun, T. Noguti anu N. uo, Rapiu Calculation of Fiist anu Seconu Beiivatives of
Confoimational Eneigy with Respect to Biheuial Angles foi Pioteins: ueneial Recuiient Equations,
C)D49*+2" R C-+D."*20, H, 2S9-247 (1984)

T. Noguti anu N. uo, A Nethou of Rapiu Calculation of a Seconu Beiivative Natiix of Confoimational
Eneigy foi Laige Nolecules, BA E-0"A H)6A B:4:5, A<, S68S-S69u (198S)

N$NPR"#?NP 8('>N?& N'&N N$I ZJP(O&

N. L. Connolly, Analytical Noleculai Suiface Calculation, BA G44IA C20"*A, >B, S48-SS8 (198S)

N. L. Connolly, Computation of Noleculai volume, BA GDA C-+DA H)6A, >?@, 1118-1124 (198S)

N. L. Connolly, Noleculai Suifaces: A Review, available fiom the web site at
http:www.netsci.oigScienceCompchemfeatuie14.html

C. E. Kunuiot, }. W. Ponuei anu F. N. Richaius, Algoiithms foi Calculating Excluueu volume anu Its
Beiivatives as a Function of Noleculai Confoimation anu Theii 0se in Eneigy Ninimization, BA
C)D49*A C-+DA, ><, 4u2-4u9 (1991)

T. }. Richmonu, Solvent Accessible Suiface Aiea anu Excluueu volume in Pioteins, BA K)IA F.)IA, >@H,
6S-89 (1984)

L. Wesson anu B. Eisenbeig, Atomic Solvation Paiameteis Applieu to Noleculai Bynamics of Pioteins
in Solution, E2)*+.5 H6.+56+, >, 227-2SS (1992)

v. uononea anu E. 0sawa, Implementation of Solvent Effect in Noleculai Nechanics, Pait S. The Fiist-
anu Seconu-oiuei Analytical Beiivatives of Excluueu volume, BA K)IA H*296*A S<-+)6-+DT, =>> SuS-
S24 (1994)

K. B. uibson anu B. A. Scheiaga, Exact Calculation of the volume anu Suiface Aiea of Fuseu Baiu-
spheie Nolecules with 0nequal Atomic Rauii, K)IA E-0"A, B<, 1247-126S (1987)

K. B. uibson anu B. A. Scheiaga, Suiface Aiea of the Inteisection of Thiee Spheies with 0nequal Rauii:
A Simplifieu Analytical Foimula, K)IA E-0"A, BE, 641-644 (1988)

S. Siiuhaian, A. Nichols anu K. A. Shaip, A Rapiu Nethou foi Calculating Beiivatives of Solvent
Accessible Suiface Aieas of Nolecules, BA C)D49*7 C-+DA, >B, 1uS8-1u44 (199S)

213 "#$%&' ()*+,) -./0* 213
NGG'JQ#ON"& 8('>N?& N'&N N$I ZJP(O&

S. }. Wouak anu }. }anin, Analytical Appioximation to the Accessible Suiface Aiea of Pioteins, E2)6A
(:*IA G6:3A H6.A QHG, @@, 17S6-174u (198u)

W. Basel, T. F. Benuiickson anu W. C. Still, A Rapiu Appioximation to the Solvent Accessible Suiface
Aieas of Atoms, <+*2:-+32)5 C)D49*A K+*-)3A, >, 1uS-116 (1988)

}. Weisei, P. S. Shenkin anu W. C. Still, Appioximate Solvent-Accessible Suiface Aieas fiom
Tetiaheuially Biiecteu Neighbei Bensities, F.)4)I0D+2", A?, S7S-S8u (1999)

VJ($IN'R ?J$I#"#J$8 N$I $&#-YVJ' O&"YJI8

W. F. van uunsteien, B. }. C. Beienusen, F. Colonna, B. Peiahia, }. P. Bollenbeig anu B. Lellouch, 0n
Seaiching Neighbois in Computei Simulations of Naciomoleculai Systems, BA C)D49*A C-+DA, A, 272-
279 (1984)

F. Sullivan, R. B. Nountain anu }. 0'Connell, Noleculai Bynamics on vectoi Computeis, BA C)D49*A
E-0"A, B>, 1S8-1SS (198S)

}. Boiis, A vectoiizeu ``Neai Neighbois'' Algoiithm of 0iuei N 0sing a Nonotonic Logical uiiu, BA
C)D49*A E-0"A, BB, 1-2u (1986)

S. u. Lambiakos anu }. P. Boiis, ueometiic Piopeities of the Nonotonic Lagiangian uiiu Algoiithm foi
Neai Neighbois Calculations, BA C)D49*A E-0"A, @=, 18S-2u2 (1987)

T. A. Anuiea, W. C. Swope anu B. C. Anueisen, The Role of Long Rangeu Foices in Beteimining the
Stiuctuie anu Piopeities of Liquiu Watei, BA C-+DA E-0"A, @D, 4S76-4S84 (198S)

B. N. Theouoiou anu 0. W. Sutei, ueometiical Consiueiations in Nouel Systems with Peiiouic
Bounuaiy Conuitions, BA C-+DA E-0"A, H<, 9SS-966 (198S)

}. Baines anu P. But, A Bieiaichical 0(NlogN) Foice-calculation Algoiithm, (:*92+, <=E, 446-449
(1986)

?("J>> N$I "'($?N"#J$ O&"YJI8

P. }. Steinbach anu B. R. Biooks, New Spheiical-Cutoff Nethous foi Long-Range Foices in
Naciomoleculai Simulation, BA C)D49*A C-+DA, >A, 667-68S (199S)

R. }. Lonchaiich anu B. R. Biooks, The Effects of Tiuncating Long-Range Foices on Piotein Bynamics,
E2)*+.5", B, S2-4S (1989)

C. L. Biooks III, B. N. Pettitt anu N. Kaiplus, Stiuctuial anu Eneigetic Effects of Tiuncating Long
Rangeu Inteiactions in Ionic anu Polai Fluius, BA C-+DA E-0"A, H=, S897-S9u8 (198S)

&<NPI 8(OON"#J$ "&?Y$#K(&8

A. Y. Toukmaji anu }. A. Boaiu, }i., Ewalu Summation Techniques in Peispective: A Suivey, C)D4A
E-0"A C)DD95A, DA, 7S-92 (1996)
214 "#$%&' ()*+,) -./0* 214

T. Baiuen, L. Peieia, L. Li anu L. Peueisen, New Tiicks foi Noueleis fiom the Ciystallogiaphy Toolkit:
The Paiticle Nesh Ewalu Algoiithm anu its 0se in Nucleic Aciu Simulations, H*296*92+, @, RSSu-R6u
(1999)

T. Baiuen, B. Yoik anu L. u. Peueisen, Paiticle Nesh Ewalu: An N_log(J) Nethou foi Ewalu Sums in
Laige Systems, BA C-+DA E-0"A, DH, 1uu89-1uu92 (199S)

0. Essmann, L. Peieia, N. L. Beikowitz, T. Baiuen, B. Lee anu L. u. Peueisen, A Smooth Paiticle Nesh
Ewalu Nethou, BA C-+DA E-0"A, >?=, 8S77-8S9S (199S)

W. Smith, Point Nultipoles in the Ewalu Summation (Revisiteu), CCE$ (+1"I+**+2, EB, 18-Su (1998)
|available fiom http:www.ul.ac.ukCCPCCPSnewslettei_inuex.htmlj

S. E. Fellei, R. W. Pastoi, A. Rojnuckaiin, S. Bogusz anu B. R. Biooks, Effect of Electiostatic Foice
Tiuncation on Inteifacial anu Tianspoit Piopeities of Watei, BA E-0"A C-+DA, >??, 17u11-17u2u
(1996)

W. Webei, P. B. Bnenbeigei anu }. A. NcCammon, Noleculai Bynamics Simulations of a Polyalanine
0ctapeptiue unuei Ewalu Bounuaiy Conuitions: Influence of Aitificial Peiiouicity on Peptiue
Confoimation, BA E-0"A C-+DA F, >?E, S668-S67S (2uuu)

?J$e(-N"&I N$I N'JON"#? 8R8"&O8

N. L. Allingei, F. Li, L. Yan anu }. C. Tai, Noleculai Nechanics (NNS) Calculations on Conjugateu
Byuiocaibons, BA C)D49*A C-+DA, >>, 868-89S (199u)

}. T. Spiague, }. C. Tai, Y. Yuh anu N. L. Allingei, The NNP2 Calculational Nethou, BA C)D49*A C-+DA, H,
S81-6uS (1987)

}. Kao, A Noleculai 0ibital Baseu Noleculai Nechanics Appioach to Stuuy Conjugateu Byuiocaibons,
BA GDA C-+DA H)6A, >?D, S818-S829 (1987)

}. Kao anu N. L. Allingei, Confoimational Analysis: Beats of Foimation of Conjugateu Byuiocaibons by
the Foice Fielu Nethou, BA GDA C-+DA H)6A, DD, 97S-986 (1977)

B. B. Lo anu N. A. Whiteheau, Accuiate Beats of Atomization anu Accuiate Bonu Lengths: Benzenoiu
Byuiocaibons, C:5A BA C-+DA, EB, 2u27-2u4u (1968)

u. B. Zeiss anu N. A. Whiteheau, Beteio-atomic Nolecules: Semi-empiiical Noleculai 0ibital
Calculations anu Pieuiction of Physical Piopeities, BA C-+DA H)6A G, 1727-17S8 (1971)

>'&& &$&'-R 8#O(PN"#J$ O&"YJI8

P. Kollman, Fiee Eneigy Calculations: Applications to Chemical anu Biochemical Phenomena, C-+DA
@+!A, D=, 2S9S-2417 (199S)

B. L. Tembe anu }. A. NcCammon, Liganu-Receptoi Inteiactions, C)D49*+2" R C-+D."*20, H, 281-28S
(1984)

215 "#$%&' ()*+,) -./0* 215
W. L. }oigensen anu C. Ravimohan, Nonte Cailo Simulation of Biffeiences in Fiee Eneigy of
Byuiation, BA C-+DA E-0"A, H=, SuSu-SuS4 (198S)

W. L. }oigensen, }. K. Bucknei, S. Bouuon anu }. Tiiauo-Rives, Efficient Computation of Absolute Fiee
Eneigies of Binuing by Computei Simulations: Application to the Nethane Bimei in Watei, BA C-+DA
E-0"A, HD, S742-S746 (1988)

S. B. Fleischman anu C. L. Biooks III, Theimouynamics of Aqueous Solvation: Solution Piopeities of
Alcohols anu Alkanes, BA C-+DA E-0"A, H@, Su29-SuS7 (1987)

0. C. Singh, F. K. Biown, P. A. Bash anu P. A. Kollman, An Appioach to the Application of Fiee Eneigy
Peituibation Nethous 0sing Noleculai Bynamics, BA GDA C-+DA H)6A, >?D, 16u7-1614 (1987)

B. A. Peailman anu P. A. Kollman, A New Nethou foi Caiiying out Fiee Eneigy Peituibation
Calculations: Bynamically Nouifieu Winuows, BA C-+DA E-0"A, D?, 246u-247u (1989)

T. P. Stiaatsma, B. }. C. Beienusen anu }. P. N. Postma, Fiee Eneigy of Byuiophobic Byuiation: A
Noleculai Bynamics Stuuy of Noble uases in Watei, BA C-+DA E-0"A, HA, 672u-6727 (1986)

T. P. Stiaatsma anu B. }. C. Beienusen, Fiee Eneigy of Ionic Byuiation: Analysis of a Theimouynamic
Integiation Technique to Evaluate Fiee Eneigy Biffeiences by Noleculai Bynamics Simulations, BA
C-+DA E-0"A, HD, S876-S886 (1988)

N. Nezei, The Finite Biffeience Theimouynamic Integiation, Testeu on Calculating the Byuiation
Fiee Eneigy Biffeience between Acetone anu Bimethylamine in Watei, BA C-+DA E-0"A, HB, 7u84-7u88
(1987)

A. E. Naik anu W. F. van uunsteien, Becomposition of the Fiee Eneigy of a System in Teims of
Specific Inteiactions, BA K)IA F.)IA, <E?, 167-176 (1994)

S. Boiesch anu N. Kaiplus, The Neaning of Copmponent Analysis: Becomposition of the Fiee Eneigy
in Teims of Specific Inteiactions, BA K)IA F.)IA, <AE, 8u1-8u7 (199S)

O&"YJI8 >J' GN'NO&"&' I&"&'O#$N"#J$

N. L. Allingei, X. Zhou anu }. Beigsma, Noleculai Nechanics Paiameteis, BA K)IA H*296*A S<N?LCN?KT,
=><, 69-8S (1994)

A. }. Peitsin anu A. I. Kitaigoiousky, "7* N45C`N45C G54*34/;B O*4750f N@@B/6;4/53 45 J+X;3/6
O5B*6.B;+ 85B/0), Spiingei-veilag, Beilin, 1987

B. E. Williams, Tiansfeiable Empiiical Nonbonueu Potential Functions, in ?+E)4;B ?57*)/53 ;30
?5395+C;4/53;B &3*+X/*), Eu. by R. N. Netzgei, Spiingei-veilag, Beilin, 1981

A. T. Baglei anu S. Lifson, A Pioceuuie foi 0btaining Eneigy Paiameteis fiom Ciystal Packing, G6*:
C20"*A, :=?, 1SS6-1S41 (1974)

A. T. Baglei, S. Lifson anu P. Baubei, Consistent Foice Fielu Stuuies of Inteimoleculai Foices in
Byuiogen-Bonueu Ciystals: A Benchmaik foi the 0bjective Compaiison of Alteinative Foice Fielus, BA
GDA C-+DA H)6A, >?>, S122-S1Su (1979)
216 "#$%&' ()*+,) -./0* 216

W. L. }oigensen, }. B. Nauuia anu C. }. Swenson, 0ptimizeu Inteimoleculai Potential Functions foi
Liquiu Byuiocaibons, BA GDA C-+DA H)6A, >?B, 66S8-6646 (1984)

W. L. }oigensen anu C. }. Swenson, 0ptimizeu Inteimoleculai Potential Functions foi Amiues anu
Peptiues: Stiuctuie anu Piopeities of Liquiu Amiues, BA GDA C-+DA H)6A, >?@, S69-S78 (198S)

}. R. Naple, 0. Binui anu A. T. Baglei, Beiivation of Foice Fielus foi Noleculai Nechanics anu
Bynamics fiom (F G.&"&4 Suifaces, E2)6A (:*A G6:3A H6.A QHG, HA, SSSu-SSS4 (1988)

0. Binui anu A. T. Baglei, Biiect Evaluation of Nonbonuing Inteiactions fiom (F G.&"&4 Calculations, BA
GDA C-+DA H)6A, >>>, S149-S1S1 (1989)

&P&?"'J8"N"#? #$"&'N?"#J$8

S. L. Piice, Towaius Noie Accuiate Nouel Inteimoleculai Potentials foi 0iganic Nolecules, @+!A
C)D49*A C-+DA, >E, 22S-289 (2uuu)

C. B. Faeiman anu S. L. Piice, A Tiansfeiable Bistiibuteu Nultipole Nouel foi the Electiostatic
Inteiactions of Peptiues anu Amiues, BA GDA C-+DA H)6A, >><, 491S-4926 (199u)

C. E. Bykstia, Electiostatic Inteiaction Potentials in Noleculai Foice Fielus, C-+DA @+!A, D=, 2SS9-
2SSS (199S)

N. }. Buuek anu }. W. Ponuei, Accuiate Noueling of the Intiamoleculai Electiostatic Eneigy of
Pioteins, BA C)D49*A C-+DA, >B, 791-816 (199S)

0. Koch anu E. Egeit, An Impioveu Besciiption of the Noleculai Chaige Bensity in Foice Fielus with
Atomic Nultipole Noments, BA C)D49*A C-+DA, >B, 9S7-944 (199S)

B. E. Williams, Repiesentation of the Noleculai Electiostatic Potential by Atomic Nultipole anu Bonu
Bipole Nouels, BA C)D49*A C-+DA, D, 74S-76S (1988)

F. Colonna, E. Evleth anu }. u. Angyan, Ciitical Analysis of Electiic Fielu Noueling: Foimamiue, BA
C)D49*A C-+DA, >=, 12S4-124S (1992)

GJPN'#SN"#J$ &>>&?"8

S. Kuwajima anu A. Waishel, Incoipoiating Electiic Polaiizabilities in Watei-Watei Inteiaction
Potentials, BA E-0"A C-+DA, DE, 46u-466 (199u)

}. W. Caluwell anu P. A. Kollman, Stiuctuie anu Piopeities of Neat Liquius 0sing Nonauuitive
Noleculai Bynamics: Watei, Nethanol, anu N-Nethylacetamiue, BA E-0"A C-+DA, DD, 62u8-6219
(199S)

B. N. Beinaiuo, Y. Bing, K. Kioegh-}espeisen anu R. N. Levy, An Anisotiopic Polaiizable Watei Nouel:
Incoipoiation of All-Atom Polaiizabilities into Noleculai Nechanics Foice Fielus, BA E-0"A C-+DA, DH,
418u-4187 (1994)

217 "#$%&' ()*+,) -./0* 217
P. T. van Buijnen anu N. Swait, Noleculai anu Atomic Polaiizabilities: Thole's Nouel Revisiteu, BA
E-0"A C-+DA G, >?<, 2S99-24u7 (1998)

K. }. Nillei, Calculation of the Noleculai Polaiizability Tensoi, BA GDA C-+DA H)6A, >><, 8S4S-8SS1
(199u)

}. Applequist, }. R. Cail anu K.-K. Fung, An Atom Bipole Inteiaction Nouel foi Noleculai Polaiizability.
Application to Polyatomic Nolecules anu Beteimination of Atom Polaiizabilities, BA GDA C-+DA H)6A,
DE, 29S2-296u (1972)

}. Applequist, Atom Chaige Tiansfei in Noleculai Polaiizabilities. Application of the 0lson-Sunubeig
Nouel to Aliphatic anu Aiomatic Byuiocaibons, BA E-0"A C-+DA, D@, 6u16-6u2S (199S)

A. }. Stone, Bistiibuteu Polaiizabilities, K)IA E-0"A, AB, 1u6S-1u82 (198S)

}. N. Stout anu C. E. Bykstia, A Bistiibuteu Nouel of the Electiical Response of 0iganic Nolecules, BA
E-0"A C-+DA G, >?<, 1S76-1S82 (1998)

ON?'J8?JG#? "'&N"O&$" J> 8JPZ&$"

C. }. Ciamei anu B. u. Tiuhlai, Continuum Solvation Nouels: Classical anu Quantum Nechanical
Implementations, @+!A C)D49*A C-+DA, B, 1-72 (199S)

B.Roux anu T. Simonson, Implicit Solvation Nouels, F.)4-0"A C-+DA, @H, 1-2u (1999)

N. K. uilson, Intiouuction to Continuum Electiostatics with Noleculai Applications, available fiom
http:gilsonlab.umbi.umu.euu

8('>N?& N'&N`VN8&I 8JPZN"#J$ OJI&P8

B. Eisenbeig anu A. B. NcLachlan, Solvation Eneigy in Piotein Foluing anu Binuing, (:*92+, =>D, 199-
2uS (1986)

L. Wesson anu B. Eisenbeig, Atomic Solvation Paiameteis Applieu to Noleculai Bynamics of Pioteins
in Solution, E2)*A H6.A, >, 227-2SS (1992)

T. 0oi, N. 0obatake, u. Nemethy anu B. A. Scheiaga, Accessible Suiface Aieas as a Neasuie of the
Theimouynamic Paiameteis of Byuiation of Peptiues, E2)6A (:*IA G6:3A H6.A QHG, HE, Su86-Su9u
(1987)

}. B. Augspuigei anu B. A. Scheiaga, An Efficient, Biffeientiable Byuiation Potential foi Peptiues anu
Pioteins, BA C)D49*A C-+DA, >@, 1S49-1SS8 (1996)

-&$&'NP#S&I VJ'$ 8JPZN"#J$ OJI&P8

W. C. Still, A. Tempczyk, R. C. Bawley anu T. Benuiickson, A Semiempiiical Tieatment of Solvation foi
Noleculai Nechanics anu Bynamics, BA GDA C-+DA H)6A, >><, 6127-6129 (199u)

218 "#$%&' ()*+,) -./0* 218
B. Qiu, P. S. Shenkin, F. P. Bollingei anu W. C. Still, The uBSA Continuum Nouel foi Solvation. A Fast
Analytical Nethou foi the Calculation of Appioximate Boin Rauii, BA E-0"A C-+DA G, >?>, SuuS-Su14
(1997)

u. B. Bawkins, C. }. Ciamei anu B. u. Tiuhlai, Paiiwise Solute Bescieening of Solute Chaiges fiom a
Bielectiic Neuium, C-+DA E-0"A U+**A, <EB, 122-129 (199S)

u. B. Bawkins, C. }. Ciamei anu B. u. Tiuhlai, Paiametiizeu Nouels of Aqueous Fiee Eneigies of
Solvation Baseu on Paiiwise Bescieening of Solute Atomic Chaiges fiom a Bielectiic Neuium, BA E-0"A
C-+DA, >??, 19824-198S9 (1996)

A. 0nufiiev, B. Bashfoiu anu B. A. Case, Nouification of the ueneializeu Boin Nouel Suitable foi
Naciomolecules, BA E-0"A C-+DA F, >?E, S712-S72u (2uuu)

N. Schaefei anu N. Kaiplus, A Compiehensive Analytical Tieatment of Continuum Electiostatics, BA
E-0"A C-+DA, >??, 1S78-1S99 (1996)

N. Schaefei, C. Baitels anu N. Kaiplus, Solution Confoimations anu Theimouynamics of Stiuctuieu
Peptiues: Noleculai Bynamics Simulation with an Implicit Solvation Nouel, BA K)IA F.)IA, <HE, 8SS-848
(1998)

8(G&'GJ8#"#J$ J> ?JJ'I#$N"& 8&"8

S. }. Keaisley, An Algoiithm foi the Simultaneous Supeiposition of a Stiuctuial Seiies, BA C)D49*A
C-+DA, >>, 1187-1192 (199u)

R. Biamonu, A Note on the Rotational Supeiposition Pioblem, G6*: C20"*A, IEE, 211-216 (1988)

A. B. NcLachlan, Rapiu Compaiison of Piotein Stiuctuies, G6*: C20"*A, I=H, 871-87S (1982)

S. C. Nybuig, Some 0ses of a Best Noleculai Fit Routine, G6*: C20"*A, :=?, 2S1-2SS (1974)

PJ?N"#J$ J> "'N$8#"#J$ 8"N"&8

R. Czeiminski anu R. Elbei, Reaction Path Stuuy of Confoimational Tiansitions anu Belix Foimation
in a Tetiapeptiue, E2)6A (:*A G6:3A H6.A QHG, HB, 696S (1989)

R. S. Beiiy, B. L. Bavis anu T. L. Beck, Finuing Sauules on Nultiuimensional Potential Suifaces, C-+DA
E-0"A U+**A, >E@, 1S (1988)

K. Nullei, Reaction Paths on Nultiuimensional Eneigy Bypeisuifaces, G5MA C-+DA =5*A ?3A ?5MIA, >D,
1-1S (198u)

S. Bell anu }. S. Ciighton, Locating Tiansition States, BA C-+DA E-0"A, H?, 2464-247S (1984)

S. Fischei anu N. Kaiplus, Conjugate Peak Refinement: An Algoiithm foi Finuing Reaction Paths anu
Accuiate Tiansition States in Systems with Nany Begiees of Fieeuom, C-+DA E-0"A U+**A, >DE, 2S2-
261 (1992)

219 "#$%&' ()*+,) -./0* 219
}. E. Sinclaii anu R. Fletchei, A New Nethou of Sauule-Point Location foi the Calculation of Befect
Nigiation Eneigies, BA E-0"A C, @, 864-87u (1974)

R. Elbei anu N. Kaiplus, A Nethou foi Beteimining Reaction Paths in Laige Nolecules: Application to
Nyoglobin, C-+DA E-0"A U+**A, >=D, S7S-S8u (1987)

B. T. Nguyen anu B. A. Case, 0n Finuing Stationaiy States on Laige-Nolecule Potential Eneigy
Suifaces, BA E-0"A C-+DA, HD, 4u2u-4u26 (198S)

T. A. Balgien anu W. N. Lipscomb, The Synchionous-Tiansit Nethou foi Beteimining Reaction
Pathways anu Locating Noleculai Tiansition States, C-+DA E-0"A U+**A, ED, 22S-2S2 (1977)

u. T. Baikema anu N. Nousseau, Event-Baseu Relaxation of Continuous Bisoiueieu Systems, E-0"A
@+!A U+**A, @@, 4SS8-4S61 (1996)