VMD-L Mailing List

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Fri Jul 16 2004 - 13:13:01 CDT

Hi John and Ray

I have hacked through solvate.tcl and found ways to make other solvent
boxes. Although they are not ideal at the beginging.

But you can replace the wat.top wat.psf wat.pdb with files describing just
one molecule of your system and slowly build an expanding box of solvent.
Each step can be minimized by namd and then more residues added until an
appriate size is found.

The solvate.tcl file has to be modified at least 4 points but no
rearrangement of the algorithm is required...

Brian

On Fri, 16 Jul 2004, John Stone wrote:

>
> Hi,
> One could probably make a modification to the "Solvate" plugin to
> use other solvents, but as you mention, you'd need a ready-made template
> solvent box for the Solvate plugin to use for this purpose. I don't personally
> know where one would be found, but perhaps someone else has a suggestion?
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Fri, Jul 16, 2004 at 10:17:23AM -0400, Raymond C. Fort Jr. wrote:
> > Is there a way to use VMD to generate a solvent box other than water? Say,
> > a simple alcohol, or a hydrocarbon?
> >
> > Or does anyone know of a site where a pdb of such a box might be downloaded?
> >
> > 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
> >
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>

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