Re: [AMBER] MMGBSA residue-wise decomposition

From: Carlos Simmerling <>
Date: Wed, 14 Mar 2012 09:05:01 -0400

these should be the same, except that the 1-4 interactions are put into
separate places. the totals should match. are you saying the total energy
does not match?

the method you should use depends very much on what you want to learn. This
is why the different options exist. If you explain what you want, we can
make suggestions.

also, you must tell us which Amber version you are using.

On Tue, Mar 13, 2012 at 7:42 AM, Rajeswari A.

> Hi Amber Developers,
> For my system when i did with idecomp 3 & 4, the total energy contribution
> of the residues are different.
> 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 am sending this query so many times since so long and awaiting for ur
> response. Somebody from Amber developing team, please do reply.
> Rajeswari A
> Computational Biophysics lab, IIT madras
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Received on Wed Mar 14 2012 - 06:30:04 PDT
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