[AMBER] Concerning nonbonded exclusions and MMPBSA

From: Aron Broom <broomsday.gmail.com>
Date: Thu, 18 Oct 2012 11:45:25 -0400

Hello AMBER users,

I'm wondering about how nonbonded exclusions are treated in MMPBSA. Are
they included just as in a normal MD run in AMBER?

The reason I ask is that I'm somewhat confused about these exclusions. I
had written my own little code to calculate just the electrostatic
potential energy portion of something in order to do part of an MMPBSA
style calculation (for reasons that are too uninteresting to go into, it is
infeasible for me to use MMPBSA or AMBER for this beyond testing
purposes). I was confused that my numbers were coming out differently from
those reported in a normal AMBER run, and tracked the problem to the fact
that I was calculating all the pairwise interactions, and while I had the
AMBER cutoff at 999 angstroms, there are still the 1-2, 1-3 complete
exclusions and the 1-4 scaled exclusions. I had thought these exclusions
were just there to save computational power because those interactions were
weak compared to the bond, angle, and dihedral components that would also
affect those atoms.

So anyway, my question basically is: if one wants to calculate the actual
electrostatic potential energy of a protein for instance, is ignoring those
exclusions accurate, or should they really be included in order to get
accurate results? And then, does MMPBSA include them?



Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Thu Oct 18 2012 - 09:00:03 PDT
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