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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 Wed, Oct 11, 2017 at 3:37 AM, sangita kachhap <nckachap.cyf-kr.edu.pl> wrote: > Thanks for the reply, Ray. > My problem is solved now. It was not the problem with AMBER but there was > some MPI problem in the computing system. > > Thanks > > On Tue, Oct 10, 2017 at 8:50 AM, Ray Luo <rluo.uci.edu> wrote: > >> Sangita, >> >> My suggestion is to use the sander option and keep the output files. >> After the new run please email the mdout files to us. So far it's hard >> to see what's going on with your runs ... >> >> All the best, >> Ray >> -- >> 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/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 Oct 11 2017 - 08:30:02 PDT