On 9/24/13 7:16 AM, aixintiankong wrote:
Dear prof.
The format of parameters is convenient to the software of Amber and
not to gromacs. if i use the parameters i must use some tools to convert it to
the itp format for gromacs. so i use acpype to get itp format.
i just doubt that i use amber99sb for protein and AM1-BBC for ligand and
resp charge for cofactor. it looks like unprofessional and i don't know
whether can affect the the MD . I do like this is right or not ?
The best method is to follow published protocols rather than trying make
something up that you hope will be right.
-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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