On 11/7/13 12:14 PM, pratibha wrote:
My protein contains metal ions which are parameterized only in gromos force
field. Since I am a newbie to MD simulations, it would be difficult for me
to parameterize those myself.
Can you please guide me as per my previous mail which out of the two
simulations should I consider more reliable-43a1 or 53a7?
AFAIK, there is no such thing as 53A7, and your original message was full of
similar typos, making it nearly impossible to figure out what you were actually
doing. Can you indicate the actual force field(s) that you have been using in
case someone has any ideas? The difference between 53A6 and 54A7 should be
quite pronounced, in my experience, thus any guesses as to what "53A7" should be
doing are not productive because I don't know what that is.
-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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