[gmx-users] MD simulation of metalloprotein

[Justin Lemkul]

On 4/28/15 1:29 AM, Biplab Ghosh wrote:
> Dear All,
>
> I am a beginner in MD and started with Gromacs. I would like to simulate
> the dynamics of a homo-dimeric
> protein containing  2 Mn atoms at the active site. I would appreciate any
> sorts of help in this regards, e.g.,
> please share your experience and/or relevant source in the web/published
> literature.
>
> Which force-filed would be appropriate? How can I take care of the metal
> ions?
>

We've had reasonably good success with AMBER Mn2+ in concert with distance 
restraints on the ligating residues:

http://www.pharmacy.manchester.ac.uk/bryce/amber

-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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