[gmx-users] Metalloenzyme MD
jalemkul at vt.edu
Tue Jan 31 19:05:36 CET 2017
On 1/31/17 1:54 AM, Reza Esmaeili wrote:
> I’m trying to simulate a metalloenzyme containing an Fe2+.
> What is the best way to make the Fe2+ stay in its place and not scape the position?
You will need to carefully parametrize bonded interactions between ligating
atoms and the ion, or at minimum set up a system of distance restraints. Or
there's always QM/MM, but that's a considerable time investment in just doing
those runs, so it depends on what the purpose of your simulation is.
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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