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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 Sun, Jan 11, 2015 at 1:26 AM, asdda asa <nadaafiva.gmail.com> wrote: > Dear Prof. Jason, > What you suppose is exatly accurate, that the nonpolar free energy > contribution were very different between PBSA and GBSA. > I already performed the free energy calculation using inp=1 for &pb section, > and it works. > Thanks so much for your help. > > best regards, > Nafiva > > On Sun, Jan 11, 2015 at 11:04 AM, Jason Swails <jason.swails.gmail.com> > wrote: > >> On Sat, Jan 10, 2015 at 10:55 PM, asdda asa <nadaafiva.gmail.com> wrote: >> >> > Dear Amber users, >> > I have problem with the result of MMPBSA and MMGBSA calculation. >> > Previously, I performed three md simulations, each consisted of a ligand >> > bound to the same protein. The three systems differ in ligand structures >> > only. >> > I noticed that there were significantly different results of binding >> > energies calculated by MMPBSA and those by MMGBSA. >> > The final binding energies calculated by GB were about -50 kcal/mol for >> > each system, while those are from PB were about +10 kcal/mol for each >> > system. >> > Please anyhelp how could these difference occured? >> > >> >> Look at the breakdown of the binding free energy contributions. I suspect >> that the nonpolar free energy contribution (ENPOLAR+EDISPER for PB and >> ESURF for GB) are very different from each other. They use different >> models by default. I suspect that you can account for almost the entire 60 >> kcal/mol difference between PB and GB binding energies simply through this >> contribution. >> >> It's unclear to me which is "better", but in this case I would probably go >> with the simple model used by GB. You can use this model in the PB code by >> setting inp=1 in the &pb section of the input file. >> >> Also make sure you are using the most up-to-date version of AmberTools. >> >> HTH, >> Jason >> >> -- >> Jason M. Swails >> BioMaPS, >> Rutgers University >> Postdoctoral Researcher >> _______________________________________________ >> 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/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Sun Jan 11 2015 - 16:30:03 PST