# Re: [AMBER] MMPBSA standard deviation (Geng Dong)

From: Ray Luo <rluo.uci.edu>
Date: Sun, 5 Jan 2020 07:46:29 -0800

Std. Err. of Mean = std. Dev/sqrt(Number of Frames Used in MMPBSA).

Please check a statistics textbook on the definitions and meanings of
the two variables.

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 Sun, Jan 5, 2020 at 3:31 AM 东庚 <gdong.stu.edu.cn> wrote:
>
> Hi all,
>
> I recently run the MM/PBSA calculations for the protein-ligand system. I confused that how to calculate the standard deviation and the standard error of mean by the MMPBSA.py. As is shown in the following the output file of MMPBSA.
>
>
> Differences (Complex - Receptor - Ligand):
> Energy Component            Average              Std. Dev.   Std. Err. of Mean
> -------------------------------------------------------------------------------
> BOND                        -0.0000                0.0001              0.0000
> ANGLE                        0.0000                0.0000              0.0000
> DIHED                       -0.0000                0.0000              0.0000
> VDWAALS                    -96.2174                6.4200              0.3700
> EEL                       -654.0075               38.7808              2.2353
> 1-4 VDW                     -0.0000                0.0000              0.0000
> 1-4 EEL                      0.0000                0.0001              0.0000
> EPB                        685.5286               40.9953              2.3629
> ENPOLAR                    -11.2411                0.4858              0.0280
> EDISPER                      0.0000                0.0000              0.0000
>
> DELTA G gas               -750.2249               39.9037              2.3000
> DELTA G solv               674.2875               40.7152              2.3468
>
> DELTA TOTAL                -75.9374               10.7729              0.6209
>
> How to obtain the std. Dev for the delta G gas (39.9037) and Std. Err. of Mean (2.3000), and  them in the Delda G solv of 40.7151 and 2.3468. Also, in the Delta total, how to obtain std. dev. of 10.7729 and std. err. of mean of 0.6209.
> Thank you very much.
>
> Best Regards,
> Geng
>
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Received on Sun Jan 05 2020 - 08:00:02 PST
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