post-processing of energy analysis

From: Katherine Wallis Abold <>
Date: Sun 7 Oct 2001 16:58:30 -0400 (EDT)

Dear Amber users,
        I am trying to obtain a breakdown of energy components by post
processing my trajectory files that I have obtained in sander_classic.
After reading about my options in Amber 6.0, I find that ANAL should be
the program of choice except that it gives inconsistent energies
(documented on the amber web page). I then was going to use MM/PBSA, but
my understanding is that it also uses ANAL to post process the data.
        My overall goal is to obtain binding data for a protein with
various ligands. I have been using the protocol outlined by

J. Wang, R. Dixon, and P. Kollman
"Ranking Ligand Binding Affinities with Avidin: A Molecular Dynamics-Based
Interaction Energy Study"
Proteins: Structure, Function, and Genetics 34:69-81 (1999)

Can anyone please suggest how to use ANAL to get consistent energies, an
alternative program, or any other options? I greatly appreciate your time.

Thanks in advance,

Katherine Abold
Graduate Student in Medicinal Chemistry
University of Michigan
Received on Sun Oct 07 2001 - 13:58:30 PDT
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