AMBER Archive (2004)

Subject: Re: AMBER: Amber8 - Energy Calculations

From: David A. Case (
Date: Thu Oct 14 2004 - 12:55:38 CDT

On Thu, Oct 14, 2004, Nhat-hang Duong wrote:
> Is there a way to calculate the energy for an atom or a residue of a
> protein?

Take a look at the anal program ($AMBERHOME/doc/anal.pdf). Note that for
many types of force fields (PME, polarizable, generalized Born), the
expressions are not pair-wise decomposable, so that the concept of the "energy
of an atom or a residue" does not make much sense.


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