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
--
==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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