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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 Wed, Sep 30, 2020 at 4:44 AM <h_sahakyan.mb.sci.am> wrote: > Dear All, > > I used MM-PBSA/GBSA methods to calculate the binding free energy between two subunits of a protein. > The binding energies were -101 and -94 kcal/mol for GBSA and PBSA respectively. However, in the > presents of a ligand (between two subunits), binding energies were -124/-67 (GBSA/PBSA). As you can > see, according to GBSA the ligand makes the interaction stronger and vice versa according to the > PBSA calculation. What can be the reason for this controversy? > > I used MMPBSA.py with following input: > > pbsa_gbsa > &general > startframe=1, interval=50, endframe=5000, > verbose=2, keep_files=0, netcdf=0, > strip_mask = ":WAT,Cl-,Na+,K+,", > ligand_mask = ":1-437,867,869", > receptor_mask = ":438-865,866,868,870", > / > &gb > saltcon=0.150, > / > &pb > inp=1 # I tried inp=2 it gives more weird results, generally with positive energy values > istrng=0.150 > / > Best wishes, > Harutyun > Senior Assistant at Laboratory of > Computational Modeling of Biological Processes, > Institute of Molecular Biology, NAS RA > 7 Hasratyan St, Yerevan, Armenia > Tel: +374 93 323990 > E-mail: h_sahakyan.mb.sci.am (h_sahakyan.mb.sci.am) > _______________________________________________ > 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 -- Senior Assistant at Laboratory of Computational Modeling of Biological Processes, Institute of Molecular Biology, NAS RA 7 Hasratyan St, Yerevan, Armenia Tel: +374 93 323990 E-mail: h_sahakyan.mb.sci.am October 1, 2020 2:57 AM, "Ray Luo" <rluo.uci.edu> wrote: > Harutyun, > > Which version of Amber are you using? Also, it's better for us to see > your detailed energy output ... > > 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 Wed, Sep 30, 2020 at 4:44 AM <h_sahakyan.mb.sci.am> wrote: > >> Dear All, >> >> I used MM-PBSA/GBSA methods to calculate the binding free energy between two subunits of a protein. >> The binding energies were -101 and -94 kcal/mol for GBSA and PBSA respectively. However, in the >> presents of a ligand (between two subunits), binding energies were -124/-67 (GBSA/PBSA). As you can >> see, according to GBSA the ligand makes the interaction stronger and vice versa according to the >> PBSA calculation. What can be the reason for this controversy? >> >> I used MMPBSA.py with following input: >> >> pbsa_gbsa >> &general >> startframe=1, interval=50, endframe=5000, >> verbose=2, keep_files=0, netcdf=0, >> strip_mask = ":WAT,Cl-,Na+,K+,", >> ligand_mask = ":1-437,867,869", >> receptor_mask = ":438-865,866,868,870", >> / >> &gb >> saltcon=0.150, >> / >> &pb >> inp=1 # I tried inp=2 it gives more weird results, generally with positive energy values >> istrng=0.150 >> / >> Best wishes, >> Harutyun >> Senior Assistant at Laboratory of >> Computational Modeling of Biological Processes, >> Institute of Molecular Biology, NAS RA >> 7 Hasratyan St, Yerevan, Armenia >> Tel: +374 93 323990 >> E-mail: h_sahakyan.mb.sci.am (h_sahakyan.mb.sci.am) >> _______________________________________________ >> 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 Wed Sep 30 2020 - 21:30:02 PDT