Dear Shu-Qing,
Actually I didn't get what you are asking ... are you following the
mmpbsa tutorial for your binding free energy calculation?
All the best,
Ray
==========================================
Ray Luo, Ph.D.
Associate Professor
Dept Molecular Biology & Biochemistry
University of California, Irvine, CA 92697
USPS: PO Box 3900 Email: rluo.uci.edu
Phones: (949) 824-9528, 9562
Web: http://rayl0.bio.uci.edu/
==========================================
shuqing wang wrote:
> Dear Amber users:
> I am a new user of Amber, now try to compute the binding free energy of the peptides system which are extracted from the GP41, for example the pdb code(1env). The receptor is the core three N-terminal called 3N,the peptide drug is T20, a HIV-1 inhibitor.(see attachment)
> I want to know weather the amber program take the peptides as one ball protein?
> which module of Amber can do this computation?
> My result of PBSA in attachment file, and the PBSUR too big can not as the experiment result. who know the reason.
> Best!
> SQ
>
>
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Received on Mon Sep 14 2009 - 13:43:15 PDT
