[gmx-users] Sigma and Epsilon values for nonbonded interactions with Fe in 2Fe2S cluster
jalemkul at vt.edu
Wed May 27 22:33:29 CEST 2015
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
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 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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