On 5/27/15 11:22 AM, Raj D wrote:
Hi , I am currently doing simulation of Fe dependent enzyme using Amber ff and I too had problem and copied sigma and Epsilon from OPLS ff and so for my simulation goes on fine.
Note that those parameters are not official OPLS (and are being removed anyway because of this fact) and certainly shouldn't be copied around between force fields. Just because the simulation doesn't crash doesn't mean it's a valid physical model.
The reference for the parameters is given in the .atp file and indicates validation in the context of Fe2+ hydrates and nothing else. The level of theory may be compatible with OPLS, but that remains to be determined. I would not think the same parameters would necessarily be valid for any other Fe-containing prosthetic group. The LJ parameters are probably of less concern than the problems associated with charges in such species.
-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.
