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

Simone Cirri simonecirri at gmail.com
Fri Mar 19 13:32:03 CET 2010

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

More information about the gromacs.org_gmx-users mailing list