On 11/8/13 3:32 PM, Williams Ernesto Miranda Delgado wrote:
Greetings again
If I use a salt concentration for neutralizing the protein-ligand complex
and run MD using PME, and the ligand is neutral, do I perform ligand MD
simulation without adding any salt concentration? It could be relevant for
LIE free energy calculation if I don't include salt in ligand (neutral)
simulation, even when I simulate Protein-ligand system with salt?
My assumption would be that you should introduce as few differences as possible.
Consider what LIE is doing - it is attempting to estimate the free energy of
binding from simple interaction energies. If you determine the strength of the
ligand-protein interaction in the presence of some higher ionic strength medium,
and then determine only the strength of ligand-water interactions rather than
the interaction of the ligand with the same medium, then I'd say the calculation
is flawed. Think of what is really happening in real life - the ligand has to
partition out of the solvent and into the protein's binding site. The solvent
is uniform throughout that process.
-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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