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-- Ray Luo, Ph.D. Professor of Structural Biology/Biochemistry/Biophysics, Chemical and Materials Physics, Chemical and Biomolecular Engineering, Biomedical Engineering, and Materials Science and Engineering Department of Molecular Biology and Biochemistry University of California, Irvine, CA 92697-3900 On Sun, Jun 28, 2020 at 5:12 AM Elvis Martis <elvis_bcp.elvismartis.in> wrote: > > Hi > MMPBSA calculations are also sensitive to internal dielectric (indi value). > You might want to look at what suits your system. > Look at this paper https://pubs.acs.org/doi/abs/10.1021/ci100275a to decide > what might be suitable for your system. > Best Regards > Elvis > > > > On Sun, 28 Jun 2020 at 17:37, Nada Afiva <nadaafiva.gmail.com> wrote: > > > Dear SIr, > > Thanks so much for your suggestions. > > However, using the above input, the result is not improved. > > Attached is the summary file for mmpbsa and mmgbsa binding energy. > > Looking forward to hearing from you. > > > > Best regards, > > Nadaafiva > > > > Pada tanggal Sab, 27 Jun 2020 pukul 22.21 Ray Luo <rluo.uci.edu> menulis: > > > > > Nadaafiva, > > > > > > There are two differences in your mmpbsa and mmgbsa setups. > > > > > > 1) The radii are different. Please set radiopt=0 to use the values in > > > the prmtop file as in the mmgbsa job. > > > > > > 2) The nonpolar term is also different. Please set > > > "cavity_surften=0.005, cavity_offset=0.000" to be the same as in the > > > mmgbsa job. > > > > > > Please use the latest AmberTools releases, as we have set the default > > > input options to be consistent between the two calculations. > > > > > > All the best, > > > Ray > > > -- > > > Ray Luo, Ph.D. > > > Professor of Structural Biology/Biochemistry/Biophysics, > > > Chemical and Materials Physics, Chemical and Biomolecular Engineering, > > > Biomedical Engineering, and Materials Science and Engineering > > > Department of Molecular Biology and Biochemistry > > > University of California, Irvine, CA 92697-3900 > > > > > > On Fri, Jun 26, 2020 at 11:01 PM Nada Afiva <nadaafiva.gmail.com> wrote: > > > > > > > > Dear Sir, > > > > Attached is the summary file in which mmgbsa is -19.1462, while mmpbsa > > is > > > > 9.2735. > > > > Thanks. > > > > > > > > Best regards, > > > > Nadaafiva > > > > > > > > > > > > Pada tanggal Jum, 26 Jun 2020 pukul 22.20 Ray Luo <rluo.uci.edu> > > > menulis: > > > > > > > > > Hi Nadaafiva, > > > > > > > > > > Can you share the summary file with all the components, not just the > > > > > total energy? > > > > > > > > > > All the best, > > > > > Ray > > > > > -- > > > > > Ray Luo, Ph.D. > > > > > Professor of Structural Biology/Biochemistry/Biophysics, > > > > > Chemical and Materials Physics, Chemical and Biomolecular > > Engineering, > > > > > Biomedical Engineering, and Materials Science and Engineering > > > > > Department of Molecular Biology and Biochemistry > > > > > University of California, Irvine, CA 92697-3900 > > > > > > > > > > On Thu, Jun 25, 2020 at 6:12 PM Nada Afiva <nadaafiva.gmail.com> > > > wrote: > > > > > > > > > > > > Yes Sir, it improved, by still the mmpbsa energy was positive. > > > > > > How the large difference occurred, and how to handle it. > > > > > > > > > > > > > > > > > > best, > > > > > > nadaafiva > > > > > > > > > > > > Pada tanggal Jum, 26 Jun 2020 pukul 07.00 Ray Luo <rluo.uci.edu> > > > > > menulis: > > > > > > > > > > > > > Dear Nadaafiva, > > > > > > > > > > > > > > This is because your NP term is different between PB and GB runs. > > > If > > > > > > > you set inp=1, the numbers would agree better. > > > > > > > > > > > > > > All the best, > > > > > > > Ray > > > > > > > -- > > > > > > > Ray Luo, Ph.D. > > > > > > > Professor of Structural Biology/Biochemistry/Biophysics, > > > > > > > Chemical and Materials Physics, Chemical and Biomolecular > > > Engineering, > > > > > > > Biomedical Engineering, and Materials Science and Engineering > > > > > > > Department of Molecular Biology and Biochemistry > > > > > > > University of California, Irvine, CA 92697-3900 > > > > > > > > > > > > > > On Thu, Jun 25, 2020 at 3:09 PM Nada Afiva <nadaafiva.gmail.com> > > > > > wrote: > > > > > > > > > > > > > > > > Dear list, > > > > > > > > I am performing MM-PBSA and MM-GBSA binding energy calculation > > > using > > > > > > > input > > > > > > > > file below. > > > > > > > > However, I got final MM-GBSA=-23.15 kcal/mol, while MM-PBSA > > > =+11.43 > > > > > > > kcal/mol > > > > > > > > I used single trajectory of MD, and obtained ligand and > > receptor > > > > > > > topology > > > > > > > > using Ante-MMPBSA. > > > > > > > > > > > > > > > > Here is the input file: > > > > > > > > > > > > > > > > Input file for running MMPBSA > > > > > > > > |&general > > > > > > > > | startframe=0, endframe=10000, keep_files=2, interval=100, > > > > > > > > | verbose=2, > > > > > > > > |/ > > > > > > > > |&gb > > > > > > > > | igb=5, saltcon=0.1, > > > > > > > > |/ > > > > > > > > |&pb > > > > > > > > | istrng=0.1, exdi=80, indi=1.0, > > > > > > > > inp=2, cavity_surften=0.0378, cavity_offset=-0.5692, > > > > > > > > fillratio=4.00, scale=2.0 > > > > > > > > linit=1000, prbrad=1.4, radiopt=1, > > > > > > > > |/ > > > > > > > > > > > > > > > > > > > > > > > > Thanks in advance. > > > > > > > > Best regards, > > > > > > > > nadaafiva > > > > > > > > _______________________________________________ > > > > > > > > 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/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/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/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 Jun 28 2020 - 10:00:03 PDT