Re: AMBER: solvation free energies using mmpbsa

From: Ray Luo <>
Date: Wed, 27 Oct 2004 21:06:07 -0700

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.
Why not use thermodynamic integration in sander? You can compute
solvation free energy of ethanol in explicit solvent without post


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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Received on Thu Oct 28 2004 - 19:53:00 PDT
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