From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Tue Oct 26 2004 - 15:02:51 CDT

Hi Jeremy
Do you have a ligand or salts present in the original pdb file?
It seems that you have something in the pdb file that is not described in
the topology file.

Regards
Brian

On Tue, 26 Oct 2004, jin wrote:

> hello,
> I am trying to generate the pdb and psf file for protein 4HVP, but I am
> getting errors using the psfgen command. I'll describe what I have done so
> far.
>
> 1)I downloaded the pdb file for 4HVP and loaded in VMD, and generated hvpp.pdb
> file for 4hvp without hydrogen bond.
> 2)I then try to create a psf file using a psfgen command on 'hvp.pgn' file I
> generated from the NAMD tutorial file. I also downloaded the topology file
> 'top_all27_prot_lipid.inp'.
>
> The script for hvp.pgn :
> package require psfgen
> topology top_all27_prot_lipid.inp
> alias residue HIS HSE
> alias atom ILE CD1 CD
> segment U {pdb hvpp.pdb}
> coordpdb hvpp.pdb U
> guesscoord
> writepdb hvp.pdb
> writepsf hvp.psf
>
> 3) when I type 'psfgen hvp.pgn', it gave me follow errors:
>
> unknown residue type ABA
> duplicate residue key PRO
> duplicate residue key IGN
>
> the list goes on with many duplicate residue keys and it ends saying the the
> molecule was destroyed bay Fatal error. Is there something I'm doing wrong?
> Please help, I appreciate it
>
> thank you,jeremy
>

*****************************************************************
**Brian Bennion, Ph.D. **
**Computational and Systems Biology Division **
**Biology and Biotechnology Research Program **
**Lawrence Livermore National Laboratory **
**P.O. Box 808, L-448 bennion1_at_llnl.gov **
**7000 East Avenue phone: (925) 422-5722 **
**Livermore, CA 94550 fax: (925) 424-6605 **
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