On 7/25/13 12:51 AM, Albert wrote:
Hello:
I notice that the manual or tutorial in Gromacs (FEP, unbralla sampling, TI
and so on) website for binding energy evaluation are all for protein in water. I
am just wondering how can we evaluate the protein/ligand binding affinity for
membrane system accurately? Probably the most difficult thing is to evaluate the
term from protein/lipids and protein/water part, since the system is
heterogeneous instead of homogeneous.
Have a look through the literature to see what other people do. The Gromacs
manual and tutorials are not going to be definitive sources for everything, nor
do they claim to be. Probably PMF is the way to go.
-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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