VMD-L Mailing List

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Fri Jul 16 2004 - 13:35:28 CDT

Thats a good place to start.
The fourth place to edit the solvate.tcl is the routine that deletes
solvent molecules that are too close to previously placed atoms. You need
to replace resname OH2 with your solvent.

Brian

On Fri, 16 Jul 2004, Raymond C. Fort Jr. wrote:

> Axel Kohlmeyer pointed out that the Gromacs website
>
> (http://www.gromacs.org/topologies/molecules.php)
>
> has some solvent boxes in .gro format, which can be converted by VMD to
> .pdb. The program VEGA
>
> http://www.ddl.unimi.it/
>
> also comes with some small boxes of several nonpolar solvents.
>
> So what it looks like to me is that I have to write by hand a charmm
> topology file for each solvent molecule, use VMD with that and the .pdb box
> with psfgen to get a .psf file, and then modify the solvate script. I
> noticed three places to modify it, which were just changing the names of
> the .pdb, .psf, and .top files.
>
> Fun for a Friday afternoon, or a Saturday morning, or whatever.....
>
> Ray
>
>
> Professor Ray Fort Jr. rcfort_at_maine.edu
> Department of Chemistry chemistry.umeche.maine.edu/fort.html
> University of Maine Voice: (207)-581-1180
> Orono, ME 04469 FAX: (207)-581-1191
>
> Computer modeling of organic and biomolecules; chemistry of lignin
> and cellulose
>
>

*****************************************************************
**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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