[gmx-users] Fe2+ non bonded parameters for AMBER

Justin Lemkul 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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