[gmx-users] parametrization of protein-ligand covalent bond

[Justin Lemkul]

On 3/22/15 6:35 PM, Leandro Bortot wrote:
> Dear users,
>
>       I need to simulate an inhibitor covalently bound to a protein. What is
> the best approach to get the parameters for adequately modeling the
> protein-ligand bond and the new residue partial charges?
>
>       I was thinking about doing a standard parametrization using the ligand
> attached to the residue as my chemical entity. By doing this, I should have
> the parameters for the bond and the new partial charges.
>

Sounds reasonable.  What does the parametrization for the parent force field 
call for?

-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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