[gmx-users] Non standard or modified amino acids

[Justin Lemkul]

On 12/22/15 9:49 AM, sun wrote:
> Hello all
> I am doing a protein peptide MD. Can anyone suggest how to obatin topology file for modified peptides or non-standard amino acids?
>

Parametrize them according to whatever methods are required by the parent force 
field.  Most modified amino acids can be constructed by analogy but should be 
verified using the force field's protocols using good target data.

-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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