VMD-L Mailing List

From: Aziz, John (John.Aziz_at_acphs.edu)
Date: Mon Mar 01 2010 - 08:27:10 CST

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>