VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Mar 03 2010 - 10:47:52 CST

Hi,
  Since you're trying to build a structure that isn't automatically
recognized by autopsf, you will have to run psfgen commands yourself to
build the PSF file using the right CHARMM parameters etc. Here are some
documentation links you will likely find to be helpful:
  http://www.ks.uiuc.edu/Research/vmd/plugins/psfgen/
  http://www.ks.uiuc.edu/Training/Tutorials/science/topology/topology-html/
  http://www.ks.uiuc.edu/Training/Tutorials/

Cheers,
  John stone
  vmd_at_ks.uiuc.edu

On Mon, Mar 01, 2010 at 09:27:10AM -0500, Aziz, John wrote:
> Hello,
> I am new to this mailing list and I am experiencing some problems with the Automatic PSF builder.
> How to generate a PSF for a molecule (i.e. Glycerin, Sucrose) that is not protein, DNA or RNA if I have the PDB?
>
> I have some PDB files for simple molecules (no amino acids, no nucleic acids and no chains) and I am trying to solvate any of them, but in order to do that, first I have to create a PSF file, and it keep giving me an error.
>
> The error message from the VMD:
>
> Error: ERROR: failed on end of segment
> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
> while excuting
> "segment $segid {
> pdb $segfile
> OR
> Error: bad index " ": must be integer?[+]integer? or end?[+]integer?
> while executing
> "lset bondorders $atom1 $ind2 $bondorder"
> (procedure "::Paratool::vmd_addbond" line 35)
> invoked from within
> "::Paratool::vmd_addbond $ind0 $ind1 $molid -2.0"
> (procedure "read_pdb_conect" line 100)
>
>
> The error message from the (fedora) Terminal:
>
> building segment O1
> reading residues from pdb file Glycerin_autopsf-temp.pdb_O1.pdb
> unknown residue type
> extracted 1 residues from pdb file
> setting patch for first residue to NONE
> setting patch for last residue to NONE
> Info: generating structure...
> unknown residue type
>
>
> for example, the PDB file for Glycerin (I've tried to manipulate the file to make it look like a protein):
>
> CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1
>
> ATOM 1 O GLC A 1 2.413 0.083 -0.302 1.00 0.00 O
>
> ATOM 2 CA GLC A 1 1.249 0.664 0.290 1.00 0.00 C
>
> ATOM 3 CB GLC A 1 0.000 -0.038 -0.246 1.00 0.00 C
>
> ATOM 4 O GLC A 1 -0.000 -1.402 0.180 1.00 0.00 O
>
> ATOM 5 C GLC A 1 -1.249 0.664 0.290 1.00 0.00 C
>
> ATOM 6 O GLC A 1 -2.413 0.083 -0.302 1.00 0.00 O
>
> ATOM 7 H GLC A 1 3.176 0.553 0.062 1.00 0.00 H
>
> ATOM 8 H GLC A 1 1.295 0.547 1.372 1.00 0.00 H
>
> ATOM 9 H GLC A 1 1.206 1.724 0.040 1.00 0.00 H
>
> ATOM 10 H GLC A 1 0.000 0.002 -1.336 1.00 0.00 H
>
> ATOM 11 H GLC A 1 -0.000 -1.392 1.147 1.00 0.00 H
>
> ATOM 12 H GLC A 1 -1.295 0.547 1.372 1.00 0.00 H
>
> ATOM 13 H GLC A 1 -1.206 1.724 0.040 1.00 0.00 H
>
> ATOM 14 H GLC A 1 -3.176 0.553 0.062 1.00 0.00 H
>
> END
>
>
> Thank you very much,
>
> John Aziz
> Albany College of Pharmacy and Health Sciences
> PharmD Candidate 2010
> John.Aziz_at_acphs.edu<mailto:John.Aziz_at_acphs.edu> 

-- 
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