VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Mar 16 2004 - 09:55:55 CST

Hi Kurt,
  One would normally load the PSF file first. If you have problems
loading the PSF file, send us the error messages your getting. I assume
you're fabricating the PSF file with your own code since the coarse-
grained models don't really fit any of the existing file formats well?

Another option for dealing with coarse-grained models better would be
to write a file reader plugin for VMD that reads your data from whatever
its native format it is rather than trying to express it as PSF/PDB which
is bound to be somewhat clunky.

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Mar 16, 2004 at 10:01:10AM +0100, Kurt Smith wrote:
> This should be a simple question but i can't find the answer:
> I am using a coarse grained model with a large number of atoms.
> If VMD tries to make bonds automatically it takes several minutes and
> has many error messages. How do I load the PDB and PSF files
> simulataneously? If I load the PDB first it does automatic bonds. I
> tried loading the PSF first and this had some problems too.
>
> Kurt Smith
>
>
> --
>
> Kurt Smith, Ph. D.
> Laboratory of Condensed Matter Physics and Nanostructures
> Universite Claude Bernard
> 69622 Villeurbanne, France
> tel. +33 (0)472431564
> fax. +33 (0)472432648
> ksmith_at_lpmcn.univ-lyon1.fr 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
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