[gmx-users] Converting a solvent box file from Amber

David van der Spoel spoel at xray.bmc.uu.se
Fri Mar 19 13:39:12 CET 2010

On 3/19/10 1:32 PM, Simone Cirri wrote:
> Hi everyone,
> I'm trying to set up a MD with the AMBER99 force field of a small
> protein in DMSO.
> I found suitable parameters for DMSO and AMBER and I built my dmso.itp .
> The problem comes now: to solvate my protein, I also need a dmso.gro
> solvent box. I could not find a way to obtain it, so I searched on the
> internet and found on the Gromacs website a dmso.gro for Gromos: but
> it does not have hydrogens, of course.
> Searching again, on the AMBER website I found a DMSO box optimized for
> AMBER99; its format, though, is rather weird because it is an .off
> file. AMBCONV, if I'm not mistaken, is not able to convert the .off
> format to the .gro or .pdb format.
> Do you have any idea about how I could work this out? Maybe converting
> the .off file isn't the only (nor it is the best) option; for
> instance, I also thought I'd protonate the Gromos dmso.gro, but I
> didn't quite understand how to do it considering that "protonate"
> seems to be forcefield-dependent (dependent from Gromos, of course).
> Thanks a lot
> Simone Cirri
Build one molecule, e.g. in molden. Then use genconf to generate a box, 
then equilibrate with MD.

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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