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

Faulkner, Matthew M.Faulkner at liverpool.ac.uk
Fri Sep 4 15:07:12 CEST 2015

Thank you Justin,

Do you know a suitable force field to use for a topolgy from PRODRG? I am aware that the topology from PRODRG may now be of the best quality but I want to run a short MDS as proof of concept first to see if the events I am interested in occur in a  reasonable timeframe.


From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Justin Lemkul [jalemkul at vt.edu]
Sent: 04 September 2015 13:58
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Force field selection for free Bicarbonate molecules in solution

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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