AMBER Archive (2006)

Subject: Re: AMBER: MMPBSA: magnitude of PB calculation

From: Ray Luo (
Date: Fri Feb 03 2006 - 01:49:07 CST


First thing first, have you patched all bugfixes for Amber8?

If yes, what dielectric constant did you use? Do you have lots of
charged interactions at the binding interface? If the binding interface
is dominated by charge-charge interactions, previous experiences show
that a higher dielectric constant at least 4 should be used to
compensate the lack of rotation polarization (which screens down
charge-charge interactions) due to the insufficient sampling of backbone.

Ray wrote:

>Hi all,
>I'm calculating the binding energy of a protein with a nonpolar ligand using
>MMPBSA, the results that I obtained are as follows:
>ELE -27.41 3.62
>VDW -52.37 2.66
>INT 0.00 0.00
>GAS -79.78 4.73
>PBSUR -3.37 0.22
>PBCAL -573.75 28.49
>PBSOL -577.12 28.40
>PBELE -601.16 27.46
>PBTOT -656.90 26.82
>I also performed entropy calculation using nmode, which results in an entropy
>contribution of around -5 kcal/mol (T=298) If that's the case, the overall
>absolute binding energy amounts to -650 kcal/mol,which is obviously
>non-physical. Is there any obvious anormaly in my PB results? Any
>suggestions/advice will be more than welcome.
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Ray Luo, Ph.D.
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
Office: (949)824-9528         Lab: (949)824-9562
Fax: (949)824-8551          e-mail:
Home page:

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