2011/4/4 Jesper Sørensen <lists.jsx.dk>
> Hi,
>
> I have a question about the output produced by the MMPBSA.py script from an
> alanine scanning.
>
> I think the value of the standard error is wrong - mostly because it is
> really high.
>
> RESULT OF ALANINE SCANNING: (L12A MUTANT:) DELTA DELTA G binding =
> 0.3974
> +/- 24.2708
>
> I have taken the output files and run them through my own matlab script.
> If I subtract the two columns with the "DELTA G binding" numbers I get:
>
> AVG -0.397356
> STD 0.937653
>
This standard deviation appears (?) to be a population standard deviation;
i.e. you have a list of numbers and calculate the stdev. MMPBSA.py
calculates this standard deviation in a propagation of errors type of way
(sqrt(std1**2 + std2**2 + ...)). The first approach takes into account all
of the correlation in the data (which lowers the variance), whereas the
latter approach assumes no correlation.
Hope this helps,
Jason
> The average is the same, but the STD is very different. Does anybody have a
> comment on this?
> I have performed this calculation of a lot of residues in my complex and
> they all produce +/- around 24 to 25, no matter the value of the ddG.
>
> Best regards,
> Jesper
>
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Apr 04 2011 - 09:30:05 PDT
