From: John S <s.john634.gmail.com>
Date: Tue, 23 Nov 2010 23:26:22 -0500

Dear Amber User's ,

I am using mmpbsa- binding energy calculations , for sidechain and backbone
separately with some ligands .

Sidechains and backbone are built as a single residue with repeating polymer
chain in my sample.In calculations using decomposition of free energy
contributions , it calculates per residue .Is there any way of specifying
atom names to find the decomposed values of binding energy.

I tried mmpbsa.pl and made receptor and ligand vacuum topology file with
only sidechains and only backbone.This conflicts with my original structure
or the complex.Since the sidechains and backbone are bonded and is it proper
to have topology files of each part of a single molecule.When I run my
calculations it works out with no error.I am concerned whether this is
proper or not.

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Received on Tue Nov 23 2010 - 20:30:03 PST
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