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
> >
>
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Received on Wed Oct 11 2017 - 04:00:02 PDT
