VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Mar 16 2004 - 12:46:46 CST

Kurt,
  Yeah, to write a plugin for VMD, you'll want to grab the latest
plugin source code from CVS, and have a look at the 'xyz' plugin or
one of the other simple ones to start with. From there, you can take
one of them and modify it to read your coarse-grain models directly, and
then you can make VMD load your plugin and try it out. Here's the general
documentation on building plugins:
  http://www.ks.uiuc.edu/Research/vmd/plugins/doxygen/

Let me know if you need help getting setup to build plugins etc.

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Mar 16, 2004 at 06:07:21PM +0100, Kurt Smith wrote:
> John,
> Thanks, the psf file loads fine now. it was just a glitch on my part.
> I would like to write a new plugin for reading my data instead of
> converting to pdb each time. In which directory would I do this? If
> there is code for reading other formats that i can adapt and then
> recompile VMD i can probably figure it out. Thanks,
>
> Kurt
>
> John Stone wrote:
> >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
> >
> >
>
>
>
> --
>
> 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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