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

Justin A. Lemkul jalemkul at vt.edu
Fri Mar 19 13:42:59 CET 2010

Justin A. Lemkul wrote:
> 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.

As an afterthought, you could also add a DMSO entry in ffgmx2.hdb and use the 
protonate tool to add the necessary hydrogen atoms.  There is not a force field 
dependence, per se, just that protonate happens to derive its information from 
this particular all-atom force field file.



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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