You calculation:
sqrt(25.9788**2 + 25.3805**2 + 3.5693**2) = 36.4939
assumes that the data for the three properties, total complex, total
receptor, total ligand, are uncorrelated. That is clearly not true,
since they are taken from the same MD run.
The way it is computed is to really go after the N binding energies and
then doing a regular std deviation calculation on that data set.
Also, please look in the mmpbsa paper and the manual, for an explanation
of how we go from stv dev to std error of the mean, and what assumptions
underlie our choices.
They are not always true, so caution is warranted.
adrian
On 3/28/17 1:05 PM, X Sun wrote:
> Hi,
>
>
> I am using MM/PBSA to calculate the binding free energy, but I don't understand how the standard deviation is calculated. A PB result is listed below.
>
>
> The TOTAL of Complex is -12509.3828 +- 25.9788
> The TOTAL of Receptor is -12188.9109 +- 25.3805
>
> The TOTAL of Ligand is -267.4237 +- 3.5693
>
>
> The DELTA TOTAL of Differences (Complex - Receptor - Ligand) is -53.0481 +- 4.3305
>
>
>
> Based on Propagation of Error, the mean of DELTA TOTAL is -12509.3828 - (-12188.9109) - (-267.4237) = -53.0482. This matches well with -53.0481.
>
>
> But the standard deviation of DELTA TOTAL should be sqrt(25.9788**2 + 25.3805**2 + 3.5693**2) = 36.4939. This is different from 4.3305.
>
>
> Could you help me figure out how the standard deviation of DELTA TOTAL of Differences (Complex - Receptor - Ligand) is calculated?
>
>
> Thanks,
>
>
> X Sun.
>
>
>
>
>
> POISSON BOLTZMANN:
>
>
> Complex:
> Energy Component Average Std. Dev. Std. Err. of Mean
> -------------------------------------------------------------------------------
> VDWAALS -3433.2149 24.0366 1.3878
> EEL -7901.6805 41.9859 2.4241
> EPB -1294.8821 28.4858 1.6446
> ENPOLAR 120.3947 1.1020 0.0636
>
>
> G gas -11334.8954 42.1986 2.4363
> G solv -1174.4873 27.8716 1.6092
>
>
> TOTAL -12509.3828 25.9788 1.4999
>
>
>
>
> Receptor:
> Energy Component Average Std. Dev. Std. Err. of Mean
> -------------------------------------------------------------------------------
> VDWAALS -3337.6543 23.9887 1.3850
> EEL -7708.7958 38.7443 2.2369
> EPB -1262.5429 26.6052 1.5361
> ENPOLAR 120.0821 0.9005 0.0520
>
>
> G gas -11046.4501 38.3867 2.2163
> G solv -1142.4608 26.1067 1.5073
>
>
> TOTAL -12188.9109 25.3805 1.4653
>
>
>
>
> Ligand:
> Energy Component Average Std. Dev. Std. Err. of Mean
> -------------------------------------------------------------------------------
> VDWAALS -42.8181 3.0298 0.1749
> EEL -165.9684 4.4683 0.2580
> EPB -65.0801 2.6750 0.1544
> ENPOLAR 6.4428 0.1744 0.0101
>
>
> G gas -208.7865 5.0103 0.2893
> G solv -58.6373 2.6421 0.1525
>
>
> TOTAL -267.4237 3.5693 0.2061
>
>
>
>
> Differences (Complex - Receptor - Ligand):
> Energy Component Average Std. Dev. Std. Err. of Mean
> -------------------------------------------------------------------------------
> VDWAALS -52.7425 4.8721 0.2813
> EEL -26.9163 4.5865 0.2648
> EPB 32.7409 4.0492 0.2338
> ENPOLAR -6.1302 0.3788 0.0219
> EDISPER 0.0000 0.0000 0.0000
>
>
> DELTA G gas -79.6589 6.2940 0.3634
> DELTA G solv 26.6107 3.9905 0.2304
>
>
> DELTA TOTAL -53.0481 4.3305 0.2500
>
>
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--
Dr. Adrian E. Roitberg
University of Florida Research Foundation Professor.
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Tue Mar 28 2017 - 10:30:04 PDT
