AMBER Archive (2003)Subject: Re: AMBER: Anal/MMPBSA
From: David A. Case (case_at_scripps.edu)
Date: Tue Dec 02 2003 - 19:29:46 CST
On Wed, Dec 03, 2003, Wu Yingliang wrote:
>
> Then, how to understand the difference of
> electrostatic energy between ANAL and MMPBSA?
>
You will have to be explicit about what differences you are referring to.
Look at the test cases in amber7/test/vac_rna to see an example of comparing
anal output to sander (or mm_pbsa) energies. The energies in analout.save
and mdout.min.save are the same (look for "INITIAL ENERGY COMPONENTS" in
the anal output). You can try to make similar comparisons for your system.
..dac
--
==================================================================
David A. Case | e-mail: case_at_scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
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