[gmx-users] Fe2+ non bonded parameters for AMBER
jalemkul at vt.edu
Wed Apr 15 15:17:36 CEST 2015
On 4/15/15 8:37 AM, Nataraj Balakrishnan wrote:
> Dear Justin,
> Thanks for your reply. I just came across one article which uses Fe2+ ion
> in the active site and as you mentioned they have used phorpherin structure
> to mimic the Fe2+ parameterzation but nothing mentioned explecitily other
> parameters details. They have used Amber molecular suit for their
This is pretty common. People use something they know and hope it translates
well to something else. In many cases, this works alright, but I am very
skeptical when I see this for ions. QM/MM studies have (for many years) shown
repeatedly that the additive representation of transition elements is a very
nasty hack that does not reflect reality. Coordination geometry can be made to
work through various tricks, and that may be OK depending on the situation, but
if you're looking at something in a binding site or something that is very
dynamic, these sorts of approximations can be really bad.
> simulation. So I don't know how to verify their parameters with my setup
> now I am using zn2+ parameters for Fe2+.
I really don't think that's valid.
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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