AMBER Archive (2004)

Subject: Re: AMBER: solvation free energies using mmpbsa

From: Ray Luo (rluo_at_uci.edu)
Date: Wed Oct 27 2004 - 23:06:07 CDT

Karl N. Kirschner wrote:

>Hi Again,
> I am still trying to understand the mmpbsa script in AMBER and its
>output. What I would like to accomplish is to calculate the free energy
>of solvation for a single molecule, say ethanol.
>
> Reading the manual, it appears that mmpbsa is capable of doing this by
>setting RECEPTOR flag to 1 in order to obtain an "absolute free energy"
>of the molecule and then by setting the GB flag to 1 obtain a
>"desolvation free energy" for the molecule. The output of this
>calculation includes the gas-phase energy (GAS) and an energy called
>GBTOT, which is defined as the summation of the hydrophobic
>contributions to the solvation free energy (GBSUR), the reaction field
>energy (GB), and the gas-phase energy. So, am I correct in saying the
>the free energy of solvation is then GBTOT - GAS? IF this is correct,
>then does one need to correct for entropy term that is left out the GAS
>phase part. If this is incorrect, could someone explain how I might
>find this value using mmpbsa. One last question - what temperature are
>these free energies calculated at?
>
>Thanks again.
>Karl
>
>
Why not use thermodynamic integration in sander? You can compute
solvation free energy of ethanol in explicit solvent without post
processing.

Ray 

-- 
====================================================
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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