AMBER Archive (2006)

Subject: Re: AMBER: MM/PBSA

From: Ray Luo (rluo_at_uci.edu)
Date: Fri Jul 07 2006 - 19:26:28 CDT

Hi Wei,

Electrostatic solvation energies sensitively depend on PRBRAD for
macromolecules, though this is not the case for small molecules. Since
it is impossible to directly measure/simulate electrostatic solvation
energies for macromolecules, there is no consensus on its value in PB
calculations.

Previous publications with RADIOPT=0 have mostly adopted PRBRAD=1.4, so
PRBRAD=1.4 is set as the default for RADIOPT=0. Similarly, radii from
RADIOPT=1 were optimized with PRBRAD=1.6, so it's set as the default for
RADIOPT=1. This doesn't mean you can't use a different value for your
own studies.

Best,
Ray

Wei Chen wrote:

>Hi, Everyone,
>
>I am using MM/PBSA to calculate free energies. In the PB section, do I need set
>RADIOPT = 0 when I set PRBRAD = 1.4, but RADIOPT = 1 when PRBRAD = 1.6?
>
>Does PB energy depends on temperature? How about GB? If PB or GB energy depends
>on temperature, how to change the temperature in MM/PBSA and Delphi?
>
>Thanks,
>
>Wei Chen
>
>--
>
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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: rluo_at_uci.edu
Home page: http://rayl0.bio.uci.edu/rayl/
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