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-- Ray Luo, Ph.D. Professor Biochemistry, Molecular Biophysics, Chemical Physics, Chemical and Biomedical Engineering University of California, Irvine, CA 92697-3900 On Tue, Feb 16, 2016 at 11:55 AM, Kalenkiewicz, Andrew (NIH/NICHD) [F] <andrew.kalenkiewicz.nih.gov> wrote: > Dear Amber users, > > I have been using the MMPBSA.py script to calculate a drug-protein binding energy. For the Poisson-Boltzmann results, the nonpolar term is exactly zero for all the residue-wise decompositions. This is not the case for Generalized Born (although they are still all very close to zero). > > Should I be surprised by this result and/or concerned that there is potentially a problem with the calculation? One rather unusual feature of my system is that the binding site is pretty much entirely enclosed at the interface of a protein-protein heterodimer (although water is still able to diffuse in and out of the site). I don't really know what I should expect based on this though. > > Any input would be greatly appreciated. > > Sincerely, > Andrew Kalenkiewicz > Postbaccalaureate Fellow, NICHD > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Tue Feb 16 2016 - 14:30:04 PST