Re: [AMBER] Confusion of difference EPB value of me and tutorial of MMPBSA.py

From: Ray Luo via AMBER <amber.ambermd.org>
Date: Sat, 27 Aug 2022 10:34:27 -0700

Dongxiao,

First thing first, your numbers are not printed in a way that is easy
for us to understand, so I don't know what different numbers you are
talking about.

Nevertheless, most likely the parameters are different between the
tutorial and your runs. You can check the "pb.mdout" files to see what
parameters are actually used in your EPB calculation.

The likely sources are 1) atomic radius options and 2) water probe radius.

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, Aug 26, 2022 at 9:03 PM Dongxiao Yue (LHS, 220059036) via
AMBER <amber.ambermd.org> wrote:
>
> I used same input prm files as tutorial to repeat the tutorial calculation. the input parameter file is as following:
> &general
>    endframe=50, keep_files=2,
> /
> &gb
>   igb=2, saltcon=0.100,
> /
> &pb
>   radiopt=0, istrng=0.100, inp=1, cavity_surften=0.00542, cavity_offset=-1.008
> /
> then I got the following value:
>
> All unit is kcal/mol
>
>             tutorial
>
>             me
>
> GB
>
> PB
>
> GB
>
> PB
>
> VDWAALA
>
> -56.2934
>
> -56.2934
>
>  -56.2921
>
>     -56.2921
>
> EEL
>
> -38.0300
>
> -38.0300
>
>  -38.0301
>
>     -38.0301
>
> EGB/EPB
>
> EGB: 50.2053
>
> EPB: 57.6402
>
> EGB: 50.2050
>
> EPB: 56.8405
>
> DELTA G non-polar
>
> -8.1491
>
> -5.0423
>
>  -8.2682
>
>     -5.0423
>
> DELTA G gas
>
> -94.3234
>
> -94.3234
>
>  -94.3222
>
>     -94.3222
>
> DELTA G solv
>
> 42.0562
>
> 52.5978
>
>   41.9369
>
>      51.7982
>
> DELTA G binding
>
> -52.2672
>
> -41.7256
>
>  -52.3853
>
>     -42.5240
>
> My EPB value is very different from that of tutorial. I really do not know which parameter can cause their difference. Many years past, mmpbsa.py updated the default parameter and maybe the computational method.
> Therefore, can you help me to find the reason causing the different value of me and tutuorail.
>
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Received on Sat Aug 27 2022 - 11:00:05 PDT