Re: [AMBER] MMPBSA error

From: Ray Luo <rluo.uci.edu>
Date: Mon, 9 Oct 2017 20:20:37 -0700

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
>
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Received on Mon Oct 09 2017 - 20:30:02 PDT
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