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 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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