VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Fri Jun 01 2007 - 11:00:26 CDT

Hi Karol,
the errors you're seeing indicate that you have a residue with blank
resname, which means there's no possible way to match it with a topology
file entry. You should make sure your residue has a name that
corresponds to a topology file entry. The names of atoms in the pdb file
should be just that -- types will be assigned by psfgen later. Please
see the namd tutorial and its appendices for more on how these files
interact.
Peter

Karol Kaszuba wrote:
> 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
>
>
>
>