AMBER: solvation free energies using mmpbsa

From: Karl N. Kirschner <>
Date: Thu, 28 Oct 2004 13:15:38 -0400

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 Nicholas Kirschner, Ph.D.
Assistant Professor of Chemistry
Hamilton College, NY 13223
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Received on Thu Oct 28 2004 - 18:53:00 PDT
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