VMD-L Mailing List

From: Rabab Toubar (rtoubar_at_yahoo.com)
Date: Thu Sep 11 2008 - 21:35:53 CDT

Hi,
 
I am trying to generate the psf file for a protein with disulfide bonds. I am using the following script:
 
package require psfgen
topology top_all22_prot.inp
alias atom ILE CD1 CD
segment U {pdb dfnp.pdb}
coordpdb dfnp.pdb U
guesscoord
writepdb dfn.pdb
writepsf dfn.psf
mol load psf dfn.psf pdb dfn.pdb
 
This gives me the following notes while generating the psf file:
 
Main console display active (Tcl8.4.1 / Tk8.4.1)
(alpha) 1 % play build.vmd
reading topology file top_all22_prot.inp
 
>>>>>>>>CHARMM22 All-Hydrogen Topology File for Proteins <<<<<<
>>>>>>>>>>>>>>>>>>>>> December 2003 <<<<<<<<<<<<<<<<<<<<<<<<<<<<
 All comments to ADM jr. via the CHARMM web site: www.charmm.org
               parameter set discussion forum
 
Created by CHARMM version 22 1
building segment U
reading residues from pdb file dfnp.pdb
extracted 30 residues from pdb file
Info: generating structure...
Info: skipping improper N-C-CA-HN at beginning of segment.
Info: skipping conformation C-N-CA-C at beginning of segment.
Info: skipping conformation C-CA-N-HN at beginning of segment.
Info: skipping bond C-N at end of segment.
Info: skipping improper C-CA-N-O at end of segment.
Info: skipping conformation CA-C-N-CA at end of segment.
Info: skipping conformation N-CA-C-O at end of segment.
Info: skipping conformation N-CA-C-N at end of segment.
Info: segment complete.
reading coordinates from pdb file dfnp.pdb for segment U
Warning: failed to set coordinate for atom CD1        ILE:7    U
Warning: failed to set coordinate for atom CD1        ILE:11              U
Warning: failed to set coordinate for atom CD1        ILE:21              U
Warning: failed to set coordinate for atom O CYS:31            U
Warning: failed to set coordinate for atom OXT       CYS:31            U
Info: guessing coordinates for 241 atoms (11 non-hydrogen)
Warning: poorly guessed coordinates for 5 atoms (2 non-hydrogen):
Warning: poorly guessed coordinate for atom HT1   ASP:2   U
Warning: poorly guessed coordinate for atom HT2   ASP:2   U
Warning: poorly guessed coordinate for atom HT3   ASP:2   U
Warning: poorly guessed coordinate for atom OT1   CYS:31            U
Warning: poorly guessed coordinate for atom OT2   CYS:31            U
Info: writing pdb file dfn.pdb
Info: Atoms with guessed coordinates will have occupancy of 0.0.
Info: pdb file complete.
Info: writing psf file dfn.psf
total of 471 atoms
total of 477 bonds
total of 844 angles
total of 1240 dihedrals
total of 69 impropers
total of 0 cross-terms
Info: psf file complete.
 
-- And I end up losing the disulfide bonds found in the original molecule. Any suggestions how to correct the errors and fix the problem of the disulfides?
 
Thanks
Rabab