Thanks a lot. Now I see.
Wei Liu
On 2015-09-15 22:30, Jason Swails wrote:
> 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
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Received on Tue Sep 15 2015 - 18:30:03 PDT
