Re: [AMBER] Very low MMPBSA result

From: Ray Luo <rluo.uci.edu>
Date: Fri, 10 Apr 2020 15:37:31 -0700

Nadaafiva,

I think there is something wrong with your calculation as the bond
term is very large.

You may want to visualize your solvent/ion-free inpcrd/prmtop files to
see if there is anything wrong with your definitions of ligand and
receptor.

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 Fri, Apr 10, 2020 at 2:20 PM Nada Afiva <nadaafiva.gmail.com> wrote:
>
> Dear Amber list,
> I would like to ask you why the MMPBSA result calculation is very low.
> The protein consisted of 3 chains.
> Here is the result:
>
> Differences (Complex - Receptor - Ligand):
> Energy Component            Average              Std. Dev.   Std. Err. of
> Mean
> -------------------------------------------------------------------------------
> BOND                     -1513.5105              991.7405
> 49.5252
> ANGLE                      -75.0126               35.0680
>  1.7512
> DIHED                      -16.8837                3.6245
>  0.1810
> VDWAALS                    -23.7054                5.0137
>  0.2504
> EEL                        -96.9434               13.9892
>  0.6986
> 1-4 VDW                      0.1667                0.0543
>  0.0027
> 1-4 EEL                      4.8667                0.3734
>  0.0186
> EPB                        116.8118               11.7134
>  0.5849
> ENPOLAR                     -3.8042                0.1633
>  0.0082
> EDISPER                      0.0000                0.0000
>  0.0000
>
> DELTA G gas              -1721.0221             1009.5413
> 50.4141
> DELTA G solv               113.0076               11.6352
>  0.5810
>
> DELTA TOTAL              -1608.0146             1010.1913
> 50.4465
>
> Here the input:
> |Input file for running MMPBSA
> |&general
> |   startframe=20000, endframe=40000, keep_files=2, interval=50,
> |   verbose=2,
> |/
> |&gb
> |   igb=5, saltcon=0.100
> |/
> |&pb
> |   istrng=0.100, fillratio=4.00, inp=1,
>
>
> Thank you.
> Nadaafiva
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Received on Fri Apr 10 2020 - 16:00:02 PDT