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.
Regards, Matthew. ________________________________________ From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: 04 September 2015 13:58 To: gmx-us...@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 -- ================================================== 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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.