AMBER Archive (2007)

Subject: AMBER: Energy calculations.

From: Karen Callahan (graylavender_at_yahoo.com)
Date: Thu Oct 18 2007 - 14:15:29 CDT

Hi,

I have a question which is another flavor of one on
the mail reflector. Would it be possible to output the
energy of the interaction between two residues or
atoms or molecules, etc, where they were solvated by
something else, say water?

Karen

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.

....dac

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