VMD-L Mailing List

From: Karol Kaszuba (karol.kaszuba_at_uwm.edu.pl)
Date: Fri Jun 01 2007 - 05:29:53 CDT

Hello!

I encountered some problems during PSF and PDB files building in VMD.
I edited topology file and I introduced the information about new residue (ligand).

When I run psfgen I noticed the following error (below).
Does anyone knows what does mean?

1) Unknown residue type means:
a) unknown res.type extracted from pdb file ?
b) unknown res.type extracted from topology file ?

2) In pdb file submitted to psfgen I should label atoms of my ligand as a:
a) types - types these same as I specified in topology file?
or
b) names - names these same as I specified in topology file?
c) maybe both types of information I should introduce in pdb file ?


Thank you in advance,
Karol Kaszuba

Created by CHARMM version 27 1
building segment U
reading residues from pdb file ISOP.pdb
unknown residue type
unknown residue type
unknown residue type
unknown residue type
unknown residue type
unknown residue type
unknown residue type
unknown residue type
unknown residue type
duplicate residue key 1
ERROR: failed on residue  from pdb file
duplicate residue key 2
ERROR: failed on residue  from pdb file
duplicate residue key 3
ERROR: failed on residue  from pdb file
extracted 12 residues from pdb file
Info: generating structure...
unknown residue type
ERROR: failed on end of segment
MOLECULE DESTROYED BY FATAL ERROR!  Use resetpsf to start over.

MOLECULE MISSING!  Use resetpsf to start over.

MOLECULE MISSING!  Use resetpsf to start over.

MOLECULE MISSING!  Use resetpsf to start over.

MOLECULE MISSING!  Use resetpsf to start over