AMBER Archive (2008)

Subject: Re: AMBER: Huge difference between pbtot and gbtot in mm-pbsa calculations

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Thu Oct 30 2008 - 06:24:12 CDT

On Thu, Oct 30, 2008, moitrayee_at_mbu.iisc.ernet.in wrote:

>
>
> # COMPLEX RECEPTOR LIGAND
> # MEAN STD MEAN STD MEAN STD
> # ======================= ======================= =======================
> PBELE -11842.66 34.34 -11842.78 35.19 36.91 4.01
> GBELE -11909.85 29.47 -11850.11 29.51 45.86 3.86

In some respects, these are not "huge differences", but rather an indication
of how sensitive these electostatic calculations can be to small changes in
the solvation algorithm. Of course, you should double-check your input and
output files, but my guess is that you are seeing a version of the situation
described here:

%A H. Gohlke
%A D.A. Case
%T Converging Free Energy Estimates: MM-PB(GB)SA Studies on the
Protein-Protein Complex Ras-Raf
%J J. Comput. Chem.
%V 25
%P 238-250
%D 2004

You might try different GB variants, but you may also just be in a situation
of subtracting large numbers in an unstable way.

...good luck...dac

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