AMBER Archive (2008)

Subject: Re: AMBER: how to get the potential energy of a protein from the system

From: David A. Case (
Date: Thu Jul 31 2008 - 09:45:47 CDT

On Thu, Jul 31, 2008, TaoPaul wrote:
> I am a freshman in MD. As far as I know the resulting potential energy (
> "EPtot" in out file ) was that of the whole system rather than the protein
> if ran a MD of protien in explicit water. So I wonder to know how to
> extract the potential energy of the protein itself. Could anybody give some
> suggestions?

Most modern energy routines (including PME and generalized Born) are not
"pairwise decomposable": so they cannot be written as just a "protein part"
plus a "solvent part" plus an "interaction part".

There *are* some sorts of analyses where it makes sense to extract the
coordinates of the protein, and compute just its potential energy. The
MM-PBSA analysis option in Amber automates this process for you. But be aware
that this involves some additional approximations.


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