AMBER Archive (2006)

Subject: Re: AMBER: MM/PBSA

From: Wei Chen (gtg553p_at_mail.gatech.edu)
Date: Sat Jul 08 2006 - 13:29:06 CDT

Hi Ray,

Thanks a lot!

Do you know if PB or GB depends on temperature and how to change temperature in

Delphi?

Wei

ÒýÓÃ Ray Luo <rluo_at_uci.edu>:

> 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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