On 12/7/13 8:11 AM, Shine A wrote:
Sir,

         I am using MD to study the folding of peptides. Now I want to
modify N terminal of the peptide with acetyl group and C terminus with
amide group.How Can I do this? What are the changes I should made in
various files? Gromos96 53a6 is using for simulation.


You need to add the coordinates for the capping groups to your input coordinate file, with names that agree with the expected nomenclature of the force field.

-Justin

--
==================================================

Justin A. Lemkul, Ph.D.
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

jalem...@outerbanks.umaryland.edu | (410) 706-7441

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