Re: AMBER: how is the standard deviations calculated in mm-pbsa?

From: David A. Case <>
Date: Tue, 6 Mar 2007 17:13:55 -0800

On Tue, Mar 06, 2007, Magne Olufsen wrote:
> I got low standard deviations from complex, receptor and ligand
> (percentages). But when the difference between these three
> contributions is added in the mm-pbsa script when I perform normal
> mode anaysis I got very high standard deviations. Does anyone know
> how the standard deviations in the sum is computed?

I strongly recommend that you try this yourself: save the individual nmode
outputs, look at the TSVIB values that get, and compute the standard deviation
by hand, and compare it to what is given by the script.

As a general comment for everyone: use the mm-pbsa script to automate some
otherwise tedious calculations; but be sure that you can do everything "by
hand", to check both the scripts and your understanding of what is being done.
Everyone's first mm-pbsa calculation should be done manually.

...good luck...dac

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Received on Wed Mar 07 2007 - 06:07:47 PST
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