AMBER Archive (2007)

Subject: Re: AMBER: output

From: David A. Case (case_at_scripps.edu)
Date: Sat Jan 13 2007 - 23:38:24 CST

On Sat, Jan 13, 2007, khn _ wrote:
>
> is there any way that i could get a list of minimized
> energy for each residues or atoms in a protein (elec,
> vdw, bond, angle etc) after doing the minimization
> process using sander module? instead of the total
> energy for whole molecule as in what the general way
> of presenting the min.out file
>

The most common Amber energy functions (PME for periodic systems, GB
for non-periodic, implict solvent systems) are not pair-wise decomposable:
that is, the energy cannot be broken down into residues or atoms. (Even
for simpler, pairwise, potentials, each interaction depends on two or more
atoms, so some choices must be made to divide this into contributions from
atoms.)

In Amber, you can use mmpbsa to get an *approximate* (and somewhat arbitrary)
breakdown. But be sure that this is what you really want.

...good luck...dac

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