Installing Schrodinger software on Linux

1. Software download

The Schrodinger software can be downloaded from our web site

http://www.schrodinger.com

Select “Downloads” from the “Resources & Downloads” menu

Please make sure you select the correct OS for the machines that will be used; note that the
Windows platform has separate installation files for 32-bit and 64-bit versions.

2. Software installation

Extract the downloaded Schrodinger_Suites_<version>_Linux-x86_64.tar file:

tar xvf Schrodinger_Suites_<version>_Linux-x86_64.tar

Go into the Schrodinger_Suites_<version>_Linux-x86_64 directory and run the installer:

./INSTALL

and follow the instructions in the Installer. You will be asked to provide an installation
directory, which is where all software will be installed, as well as a temporary directory which
will be used to store temporary job files
When the installation is complete, set the SCHRODINGER environment variable:

setenv SCHRODINGER /path/to/schrodinger/installation/directory

export SCHRODINGER=/path/to/schrodinger/installation/directory

where /path/to/schrodinger/installation/directory is the directory chosen during the installation

procedure.

After installing the license (see below), Maestro can be started via the following command:
 $SCHRODINGER/maestro

3. Requesting a license

Once the software has been installed, a license will be needed in order to start Maestro and
run jobs. In order to obtain a license for the workshop, please contact, in the following order:

1) Your account manager

2) licensing@schrodinger.com
3) Call the technical support line at:
US: +1 (503) 299 1150
Europe: +49 621-438-55173

4. License Installation and verification

Make sure the SCHRODINGER environment variable is set to the top level Schrödinger
installation directory (example: /opt/schrodinger/suite2014-1) with the following
command:

bash/ksh: export SCHRODINGER=top_level_installation_directory

tcsh/csh: setenv SCHRODINGER top_level_installation_directory

If you have current licenses in your ‘$SCHRODINGER/license’ file that you do not want
replaced by the new license file, please send both the old and new license files to
help@schrodinger.com and we will send you a single file that combines all of your licenses.

Otherwise, move/copy the new license file directly to

$SCHRODINGER/license

overwriting any existing 'license.txt' file.

Node-locked license: Verifying the licenses

In a terminal window, set the SCHRODINGER environment variable to point to the top level
Schrödinger installation directory.
Start the Diagnostics user interface:

$SCHRODINGER/diagnostics

Verify that the correct licenses are reported in the "License Test" tab. If yes, you should be
able to start Maestro. If no, click on the Tech Support button at the bottom of the Diagnostics
panel and send the resulting tarball file as an attachment in an email to
help@schrodinger.com.

Server-based license: Starting/updating the license server and verifying the licenses
In a terminal window, set the SCHRODINGER environment variable to point to the top level
Schrödinger installation directory.
Start the Diagnostics user interface. $SCHRODINGER/diagnostics
If the "Stop License Server" button is enabled, click it to temporarily stop the license server
daemon.
Click the "Start License Server" button to start the license server daemon. If you are installing
server-based licenses but this button is not enabled, you might be running the Diagnostics
GUI on a machine other than the license server.
Verify that the license server daemon is running and reporting the correct licenses in the
"Server Status" tab. If yes, you should be able to start Maestro. If no, click on the Tech
Support button at the bottom of the Diagnostics panel and send the resulting tarball file as an
attachment in an email to help@schrodinger.com.

5. Checking the installation

In order to check the software installation, please run the following and check that the output
agrees whit what is seen below.

a. Check that the top level environment variable is set correctly:

echo $SCHRODINGER

This should give:

/path/to/schrodinger/installation/directory (same as in 2.)

b. Check what programs have been installed:

 $SCHRODINGER/machid

This should give output similar to:

Date: Tue Feb 18 19:41:52 2014

SCHRODINGER: /opt/schrodinger/suites2014-1
uname -a : Darwin Heges-MacBook-Pro.local 11.4.2 Darwin Kernel Version 11.4.2: Thu
Aug 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64
ERROR: Fully qualified domain name could not be obtained
FQDN: Heges-MacBook-Pro.local
IP address: 10 211 55 2
Main memory: 8185 MB
Free disk: 518980 MB
Host ID: 3c07545035d6
Machine name: Heges-MacBook-Pro.local
OS: MacOSX 10.7.5
CPU: x86_64
Processors: 4
perl: 5.014
python: 2.7
Product: bioluminate-v14012-Darwin-x86_64
Product: canvas-v19012-Darwin-x86_64
Product: combiglide-v32012-Darwin-x86_64
Product: desmond-v37012-Darwin-x86_64
Product: epik-v27012-Darwin-x86_64
Product: ffld-v13012-Darwin-x86_64
Product: impact-v62012-Darwin-x86_64
Product: jaguar-v83012-Darwin-x86_64
Product: knime-v19012-Darwin-x86_64
Product: leadopt-v13012-Darwin-x86_64
Product: macromodel-v103012-Darwin-x86_64
Product: maestro-v97012-Darwin-x86_64
Product: mcpro-v33012-Darwin-x86_64
Product: mmshare-v25012-Darwin-x86_64
Product: phase-v38012-Darwin-x86_64
Product: psp-vpsp-Darwin-x86_64
Product: qikprop-v39012-Darwin-x86_64
Product: scisol-v13012-Darwin-x86_64
Product: watermap-v18012-Darwin-x86_64
Module: python-v44012-Darwin-x86_64

c. Run the Diagnostics panel to provide information on the installation, including

license information (as seen in step 4. above)

$SCHRODINGER/diagnostics

This command will open the Diagnostics panel. There are two top-level tabs in the panel;
License and Hosts. In the License tab, we see the 'Server Status' (for server-based licenses)
and results of the License Test
 The third tab, 'Job Capacity', shows the number of allowed simultaneous jobs can be
run for each installed program. The top-level Hosts tab should show results similar
to the below, if you choose "Run test job on: 'Selected Hosts/All Hosts'"

Click the "Techsupport…" button. This will create a tarball of all your Diagonistics test.
Send your tarball output to the workshop organizer and help@schrodinger.com.

6. Installing scripts in Maestro

A number of Python scripts are available to use in Maestro and many of them are installed
with the software installation. The scripts are accessed from the Scripts… menu in Maestro

Scripts not in the default installation can be installed from Maestro:

Scripts > Update… => update scripts from the Script Center page of our web site
Scripts > Install… => install scripts from a local disk

7. Downloading KNIME Workflows and example files

If the workshop will include KNIME, please download the KNIME workflows. They are
available from our website:

www.schrodinger.com

Select “KNIME Workflows” from the “Resources & Downloads” menu

Choose the “Select All” option to download all available workflows. Please do also make
sure to toggle on the option to “Include optional example data in the download” and follow the
installation instructions on the web site.

8. Running simple test jobs

a. Simple LigPrep job that will return the output structures to the Maestro Project
Table:

 In Maestro: Project > Import Structures…

 Navigate to: <SchrodingerInstallationDirectory>/maestro-v<version>/tutorial
 Import: small_molecule.mae
 Go to Applications > LigPrep
 Select to "Use structures from: Workspace (included entries)"
 Leave all options at their default values
 Click the "gear" button next to the 'Job name:' field at the bottom at the panel and
make sure that the "Incorporate" option is set to "Append new entries" and that the job
will run on 1 processor, and is separated into 1 sub job, then click the "Save and Run"
 button to start the job.

The job will finish quickly, and eight output structures will be added to the Project Table in a
new group.

b. Simple Python script that will calculate molecular descriptors for the output
structures from step a.

 With the output compounds from the LigPrep job selected (highlighted) in the Project
Table, go to Scripts > Cheminformatics > Molecular Descriptors…
 Select to "Use structures from: Project Table (selected entries)"
 Go to the "Semiempirical Properties" tab and toggle off the option to "Compute
Semiempirical Properties"
 Click the "Run" button

The job will finish quickly, and a new group, containing eight output structures, will be added
to the Project Table. A number of new columns will also be added to the Project Table,
containing the Molecular Descriptor properties.

c. Run a simple KNIME workflow

Open Knime, then in the Node Repository:

 Go to Schrodinger > Readers/Writers and drag the “Molecule Reader” node into the
project workspace
 Go to Schrodinger > Molecular Mechanics > Minimization and drag the “MacroModel
Minimization” node into the project workspace
 Go to Schrodinger > Readers/Writers and drag the “Molecule Writer” node into the
project workspace

Connect the nodes (drag the mouse from a triangle on one node to a triangle on the next
node) so that the workflow goes from the “Molecule Reader” node to the “MacroModel
Minimization” node to the “Molecule Writer” node

 Right-click the “Molecule Reader” node and select “Configure…” from the menu
 Click the “Add File(s)…” button and select the following file:
<Schrodinger installation directory>/macromodel-v<version>/samples/Examples/ecalc.mae

where <Schrodinger installation directory> is the directory/folder in which you installed the
Schrodinger software.
 Click “OK” to exit the configuration panel

 Right-click the “Molecule Writer” node and select “Configure…” from the menu
 Type in the desired name of the output file, for instance, testKnime-out.mae
 Click “OK” to exit the configuration panel

 Select all three nodes in the workspace

 Right-click and select “Execute…” from the menu to run the workflow.

You should see some time being spent in the “MacroModel Minimization” and the output file
should be written to the directory/folder shown in the Console part of the GUI

9. Downloading the thirdparty Blast and PDB databases

Homology modeling uses the Blast and PDB databases to search for and import homologs.
It is possible to access these databases remotely by setting the preference:
Maestro > Preferences > Jobs > Starting; toggle on to “Use web server for BLAST searches”

If desired, the Blast and PDB databases can be installed locally. We provide utility scripts
that can be used to install the databases:

Blast: $SCHRODINGER/utilities/update_BLASTDB
PDB: $SCHRODINGER/utilities/rsync_pdb

In order to install the databases run the commands above. Running the commands with the
“-h” option will show usage and options for the commands:

$SCHRODINGER/utilities/update_BLASTDB -h
$SCHRODINGER/utilities/rsync_pdb –h
10. Setting Environment variables

By default, third party programs and data will be installed in $SCHRODINGER/thirdparty,

where $SCHRODINGER is the top-level directory for the software installation. If desired, third
party data (Blast and PDB databases) may be placed in non-default locations, in which case,
one has to use environment variables to point to their locations. Environment variables used
are PSP_BLASTDB for the location of the Blast database and SCHRODINGER_PDB for the
location of the PDB database. In the instructions below:

variable: PSP_BLASTDB for the Blast database

SCHRODINGER_PDB for the PDB database

value: full path to the location of the database; for instance

/home/databases/blast
/home/databases/pdb

Enter the following command at a shell prompt:

csh/tcsh: setenv variable value

bash/ksh: export variable=value

11. Firewalls and proxies

Firewalls and proxies may impact how you access the license server, remote hosts, and the
internet. Please see the Schrodinger Installation Guide for information on how to configure
firewalls and accessing the web via a proxy. The installation guide can be found in the
following location:

$SCHRODINGER/docs/general/install_guide.pdf

It can also be downloaded from our website:

http://schrodinger.com/supportdocs/18/