On 11/2/13 1:00 AM, Kavyashree M wrote:
Dear Gromacs users,
I have a protein-ligand in water simulation (Gmx 4.5.3), for
calculating free energy of ligand binding, a separate simulation
of ligand in water simulation is required (which I read from the
list). The question is the protein-ligand is simulated as a dimeric
system so is it necessary to simulate the ligand in water as
a dimer too.
Only if the ligands interact as a dimer in the bound state. If the bind in
distinct binding sites within the protein monomers, then no, that wouldn't make
much sense to do.
-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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