Re: Nanotube psf file.

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Wed Apr 06 2005 - 13:28:34 CDT

Hello,

Did you specify the correct topology file to use?

ie the command topology is present in your psfgen script

topology some_topology_file.inp

and this file has the correct residue that you are trying to build?

Brian

On Wed, 6 Apr 2005 mustapha.hamdi_at_ensi-bourges.fr wrote:

> Hi,
>
> I am trying to work with nanotubes using NAMD and VMD. Ive tried to
> generate the nanotubes psf file from the nanotubes.pdb file using PSFGEN
> from NAMD 2.5 for Win32-i686, and I obtain some errors like this:
>
> building segment A
> reading residues from pdb file tube.pdb
> unknown residue type ARM
> extracted 1 residues from pdb file
> Info: generating structure...
> unknown residue type MOL
> ERROR: failed on end of segment
> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
>
>
> Please I would like to know how to solve this problem.
>
>
> Best regards.
>
>
>
>
>

************************************************
  Brian Bennion, Ph.D.
  Bioscience Directorate
  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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