[gmx-users] Metalloenzyme MD

[Justin Lemkul]

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

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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
http://mackerell.umaryland.edu/~jalemkul

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