Re: [AMBER] Pairwise decoposition (MMPBSA)

From: Bill Miller III <>
Date: Wed, 17 Oct 2012 11:19:51 -0400

This question has been answered previously on the Amber list. See for
example, the end of this post:
Basically, although the results are printed by residue, the interactions
are actually calculated on a by-atom basis. So a residue interacts with
itself in so much as the atoms inside that residue interact with each other.

I hope that helps.


On Tue, Oct 16, 2012 at 10:34 PM, Xioling Chuang <>wrote:

> Dear All,
> I have calculated a pairwise decoposition using MMPBSA for DNA 10-mer
> duplex. The result showed the interaction, for example, of residue#1 with
> another 19 residues as well as with residue#1 itself. Could anyone tell me
> why the MMPBSA calculates the pairwise interaction with itself?
> Thank you very much in advance for your kindness.
> Best,
> Xioling
> _______________________________________________
> AMBER mailing list

Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Wed Oct 17 2012 - 08:30:03 PDT
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