Re: AMBER: Anal/MMPBSA

From: David A. Case <case.scripps.edu>
Date: Tue, 2 Dec 2003 17:29:46 -0800

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 

-- 
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David A. Case                     |  e-mail:      case.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:                   
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Received on Wed Jan 14 2004 - 15:53:04 PST
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