[gmx-users] Force field parameter for Fe, Mo, Mn, Cd, Ni and Co.

[Justin Lemkul]

On 11/19/14 10:52 PM, majid foroughi wrote:
> Hello, I am using Gromacs version 4.6.6 and GROMOS96 53a6 force field.I am
> studying a metalloprotein with zinc in active site, now I wanna substitute
> the zinc ion with other metal ions such as Fe, Mo, Mn, Cd, Ni and Co, to see
> the protein stability and other features. But cannot make topology file for
> the protein with these metal ions because the force field is not parametrised
> for these ions. Now my question is, where can I find the data required to
> parametrized these metal ions in the gromacs force field. Also I wish to be
> guided on the approach how to parametrize these metal ions.

I doubt you'll ever get a good model with a typical MM force field.  There's a 
reason the parameters aren't there already.

http://www.gromacs.org/Documentation/How-tos/Parameterization#Exotic_Species

QM/MM is probably a much better idea than plain MD.

-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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