AMBER Archive (2006)

Subject: Re: AMBER: regarding PBCAL in MM-PBSA

From: Ray Luo (
Date: Mon Oct 16 2006 - 19:35:42 CDT

Dear Jenk,

Please provide more information on your calculation. The statistics
output would be a good start.


Cenk Andac wrote:

> Dear Amber community,
> I was just wondering how one would go about interpretation of PBCAL
> values (in MMPBSA computations) for receptor and complex. PBCAL for my
> receptor has a more negative value than PBCAL for the complex. Does
> this mean that the complex experiences a lower dielectric lattice due
> to some water molecules replaced by the ligand in the binding site?
> best regards,
> jenk.
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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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