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

Raj D gromacs.for.f at gmail.com
Wed Apr 15 16:21:34 CEST 2015

Dear Jastin,
Exactly,  I would like to study few important mutants which falls well out
of Fe2+ coordinating shell and the study is about to compare dynamics of
the wild type and mutant systems and I hoping a stable simulation with a
crude approximation of active is enough for this purpose because internally
its very luxurious proposition to do QM study to derive a parameters for
Fe2+ in the active site.
Hoping your continus support for my study

 On Apr 15, 2015 6:47 PM, "Justin Lemkul" <jalemkul at vt.edu> wrote:

> 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
> --
> ==================================================
> 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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