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

Justin Lemkul jalemkul at vt.edu
Wed Apr 15 14:20:29 CEST 2015

On 4/15/15 12:19 AM, Raj D wrote:
> Dear Users,
> Had anybody used Fe2+ ions in the active site of protein. I am planning to
> use one using amber99sb forcefield...please suggest to use the nonbonded
> parameters for Fe2+ ions, sigma and epsilon values.

Most force field parameters are specifically for heme, so if they haven't been 
developed yet, you're probably out of luck without doing the parametrization 
yourself.  Additive models for transition metals are very crude, anyway.  You 
face the additional challenge of getting the electrostatics right.



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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