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

Justin A. Lemkul jalemkul at vt.edu
Fri Mar 19 13:38:59 CET 2010

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).

If you have a suitable AMBER-compatible input file, can't you convert it within 
Leap and save it as a .pdb file?  If not, use one of the many small molecule 
drawing tools (several are listed on the Gromacs site) to obtain coordinates for 
a single DMSO molecule, use genconf -nbox to generate a box, and equilibrate one 
of your own with the parameters you have available to you.


> Thanks a lot
> Simone Cirri


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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