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-- Ray Luo, Ph.D. Professor of Structural Biology/Biochemistry/Biophysics, Chemical Physics, Biomedical Engineering, and Chemical Engineering Department of Molecular Biology and Biochemistry University of California, Irvine, CA 92697-3900 On Mon, Oct 9, 2017 at 7:27 AM, sangita kachhap <nckachap.cyf-kr.edu.pl> wrote: > Dear AMBER Developer > > I am doing free energy calculation for protein-ligand complex using > amber16. I am getting all the energy values by GB calculation but not by PB > calculation. > > BOND 0.0000 0.0000 > 0.0000 > ANGLE 0.0000 0.0000 > 0.0000 > DIHED -0.0000 0.0001 > 0.0000 > VDWAALS -21.7043 3.5652 0.4603 > EEL -67.5611 13.6737 > 1.7653 > 1-4 VDW 0.0000 0.0000 > 0.0000 > 1-4 EEL 0.0000 0.0000 > 0.0000 > EPB nan nan > nan > ENPOLAR -0.5965 1.5886 0.2051 > EDISPER nan nan nan > > DELTA G gas -89.2654 12.8027 1.6528 > DELTA G solv nan nan nan > > DELTA TOTAL nan nan nan > > Herewith I am attaching mmpbsa output file. > > I also checked the water and ion striped trajectory of complex with prmtop > file (which I have used for MMPBSA calculation) in VMD, both files are > compatible. > > > Please suggest me how to solve it. > > Thanks > > _______________________________________________ > 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 Mon Oct 09 2017 - 20:30:02 PDT