[gmx-users] adding metal-bonding parameters to a force field

[Justin Lemkul]

On 4/3/14, 2:58 PM, Gmail2 wrote:
> Dear Justin,
>
> Zn bound to three Histidine atoms and a water in carbonic anhydrase. This water bound to Zn has different parameters than solvent water. That parameters is present in literature. How should I set up such a system?
>
> PS: I will use 'pdb2gmx' with -vsite hydrogens.
>

If you need virtual sites, then you need to figure out how to properly build a 
virtual site database entry for that particular type of molecule.  That's 
entirely separate from any of the force field parameters you've shown before, 
but realize that doing so negates most of the Zn-HOH bonded parameters you posted.

-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 601
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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