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 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
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