VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Sep 11 2008 - 22:33:18 CDT

Hi Rabab,
you need to explicitly generate any disulfide bonds using patch
statements, eg,

patch DISU U:res1 U:res2
where res1 and res2 are the resids that should form a disulfide bond.

Peter

Rabab Toubar wrote:
> 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
>
>