[gmx-users] Force field selection for free Bicarbonate molecules in solution

Justin Lemkul jalemkul at vt.edu
Fri Sep 4 14:58:31 CEST 2015

On 9/4/15 7:42 AM, Faulkner, Matthew wrote:
> I am trying to find a suitable force field for using Bicarbonate in an
> aqueous environment in my MDS. I can't find anything where Bicarbonate has
> been used this way in gromacs in the literature, does anybody know of a
> reference for me or have advice on which force filed would be best?
> I have run several MDS in the OPLS-AA force field for my protein of interest
> in solution with water and various ions and they work very well,but I would
> like to add 150 mM HCO3- into my environment. I have a PDB and TOP file
> prepared using PRODRG for the HCO3- but I'm not sure if the OPLS-AA force
> field is suitable for this molecule.

FWIW, PRODRG topologies are (1) very poor quality and (2) not compatible with OPLS.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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