Re: [AMBER] MMGBSA residue-wise decomposition

From: Jason Swails <>
Date: Wed, 14 Mar 2012 09:34:40 -0400


On Wed, Mar 7, 2012 at 12:18 AM, Rajeswari A.

> Dear Amber users,
> As per the manual idecomp 3 - Pairwise decomp with 1-4 terms added to
> internal potential terms
> 4 - Pairwise decomp with 1-4 EEL added to EEL and 1-4 VDW added to VDW
> potential terms.
> For my system when i did with idecomp 3 & 4 , in both cases, the internal
> potential term was 0.000 +/- 0.000. and the total energy contribution of
> the residues are different.

There are no pairwise internal potential terms, as far as I know. The
interesting values are the pairwise non-bonded potentials (particularly
VDW, EEL, and POL). Keep in mind that the POL energies are not pairwise
decomposable due to the inclusion of all atoms in the calculation of the
effective born radii, but it's a reasonable approximation. If you look at
energy values between non-adjacent residues (that is, between residues that
do not share a dihedral), the energy decompositions for idecomp=3 and
idecomp=4 should be identical. If they are not, I think there may be a
problem (note the caveat I mention below).

What happens if you ignore all of the surface tension terms? I think there
was a bug in gbsa=2 (that's been fixed recently -- I'll make a bugfix for
Amber 11 shortly) that was giving rise to this type of behavior.

1. Is my calculation correct?
> 2. which method of decomposition should i use?
> 3. what is the reason for different total energy contribution of each
> residue by different decomposition terms?

I do not understand exactly what you're seeing with #3. If you posted
parts of the relevant output files that might help. I don't understand
what is differing where, so it's hard to provide assistance.


> Please Clarify my doubts.
> Thank you very much in advance
> Rajeswari A
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Wed Mar 14 2012 - 07:00:03 PDT
Custom Search