On Tue, Sep 15, 2015 at 2:22 AM, wliu <wliu.itcs.ecnu.edu.cn> wrote:
> Dear all,
>
> I have a simple question about the output of binding free energy
> decomposition. I calculated Per-residue energy decomposition for
> specific residues with mmpbsa.py and I got the FINAL_DECOMP_MMPBSA.dat
> file.
>
> DELTAS:
> Total Energy Decomposition:
> Residue | Location | Internal | van der Waals |
> Electrostatic | Polar Solvation | Non-Polar Solv. |
> TOTAL
>
> -------------------------------------------------------------------------------------------------------------------------------------------------------
> LEU 18 | R LEU 18 | 0.000 +/- 0.000 | -2.968 +/- 0.505 |
> -0.436 +/- 0.232 | 3.215 +/- 0.453 | 0.000 +/- 0.000 | -0.189
> +/- 0.583
> GLU 20 | R GLU 20 | 0.000 +/- 0.000 | -1.521 +/- 0.431 |
> -0.527 +/- 1.684 | 0.859 +/- 1.585 | 0.000 +/- 0.000 | -1.189
> +/- 0.539
>
> Then here is my question, Does the value after +/- sign stand for
> standard deviation of the calculated energy, or standard error instead?
>
​Standard deviation. It will also compute the standard error (via std.err
= std.dev / sqrt(N) where N is the number of frames in the trajectory) and
print that if you ask for CSV format decomposition output.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Sep 15 2015 - 08:00:03 PDT
