[gmx-users] simulating AMP covalently linked to a protein

[Justin Lemkul]

On 5/24/17 7:08 PM, Gilberto Valdes wrote:
> Hi,
>
> I'm interested in simulating a DNA ligase with an AMP bound covalently via
> its P atom to the side chain of a Lysine residue. I can not find any
> parameters for that. I really appreciate any help in how to achieve this.
>

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

The details depend on which force field you've chosen to use, and that choice 
actually depends on other factors - how much chemical space that force field 
covers (e.g. how easy is it going to be to even start this venture) and how easy 
to follow are the published methods for that force field.

-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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