Crear una molecula

http://mem.bio.pitt.edu/content/building-alpha-helical-peptides-command-line-using-vmd Molden MOLDA Modeller :http://www.salilab.org/modeller/wiki/Make%20alpha%20helix Pymol: http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/ VMD: This is the TCL script: #!/usr/bin/tclsh set amseq [lindex $argv 0] mol new atoms 1 package require molefacture ::Molefacture::set_phipsi -57 -47 ::Molefacture::build_textseq $amseq set allSel [atomselect top "resid < 9999"] $allSel writepdb $amseq.pdb We set the Phi and Psi angles to the canonical alpha-helix values of -57 and -47. The Resid < 9999 is necessary because Molefacture adds in a bunch of extra atoms for visualization purposes. Now because Molefacture is geared to run as a graphical interface, you will have to make a modification for it to be run from the command-line (with vmd -dispdev text). Open up vmd/plugins/noarch/tcl/molefacture-1.1/molefacture_gui.tcl and locate line number 995. Comment out this line by prepending a pound sign (#): #set answer [tk_messageBox -message "This will abandon all editing on the current molecule. Are you sure?" -type yesno -icon question] Now add the following line immediately below it: set answer yes And now the script can be run using the following command: vmd -dispdev text < build_helix.vmd -args (amino_acid_sequence) This will write a PDB file with a filename of (amino_acid_sequence).pdb http://www.ncsu.edu/chemistry/franzen/public_html/CH795N/projects/GFP_MD.htm http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node6.html http://www.ks.uiuc.edu/Research/namd/2.7/ug/node16.html http://www.disprot.org/resource.php http://www.ks.uiuc.edu/Research/vmd/plugins/autopsf/tech.html