[gmx-users] Sigma and Epsilon values for nonbonded interactions with Fe in 2Fe2S cluster

[Justin Lemkul]

On 5/27/15 11:22 AM, Raj D wrote:
> Hi ,
> I am currently doing simulation of Fe dependent enzyme using Amber ff and I
> too had problem and copied sigma and Epsilon from OPLS ff and so for my
> simulation goes on fine.

Note that those parameters are not official OPLS (and are being removed anyway 
because of this fact) and certainly shouldn't be copied around between force 
fields.  Just because the simulation doesn't crash doesn't mean it's a valid 
physical model.

The reference for the parameters is given in the .atp file and indicates 
validation in the context of Fe2+ hydrates and nothing else.  The level of 
theory may be compatible with OPLS, but that remains to be determined.  I would 
not think the same parameters would necessarily be valid for any other 
Fe-containing prosthetic group.  The LJ parameters are probably of less concern 
than the problems associated with charges in such species.

-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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