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

[Justin Lemkul]

On 4/15/15 10:21 AM, Raj D wrote:
> 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.

Then it might be reasonable to use the nonbonded parameters from something like 
heme, perhaps in concert with distance restraints to preserve the coordination 
geometry.  Validate very carefully with well defined systems before doing a 
full-scale study.

-Justin

> Hoping your continus support for my study
>
> Thanks
> Raja
>   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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-- 
==================================================

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

==================================================