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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 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/amberReceived on Sat Jun 27 2020 - 08:30:04 PDT