AMBER Archive (2004)

Subject: Re: AMBER: MM_PBSA reproduction of literature values and accuracy

From: Karl N. Kirschner (
Date: Tue Oct 26 2004 - 17:35:19 CDT

Hi Carlos and Thomas,
  Thanks for you replies so far. From my understanding, the mmpbsa
script is capable of calculating an absolute free energy (ie. RECPT is
set to 1 in while Complex and Ligand are set to 0) using the
GB model in sander. The gas-phase values are not subtracted out (GBTOT
= GBSUR + GB + GAS, where GBSUR is the hydrophobic contribution to
solvation free energy, GB is reaction field energy, and GAS is ELEC +
VDW + INT). The entropy contributions are not included in GBTOT.

  The entropy contributions are calculated using NMODE. This is done
for each snapshot of ethanol pulled from the explicit solvation dynamics
(ie. on ~1000 structures). To be clear, I generate an ensemble of
ethanol conformations using explicit solvation dynamics and then
calculate the GBTOT and the entropy on just the ethanol (ie. the TIP3P
waters are not included in the post trajectory mmpbsa calculation) from
each saved structure in the ethanol_water_md.crd coordinate file.

  So, maybe I am trying to use mmpbsa to answer a question that I
shouldn't. But, I was under the impression that one can calculate a
free energy of solvation for a molecule using the mmpbsa script.

  Thanks again for talking this through...


Karl Nicholas Kirschner, Ph.D.
Assistant Professor of Chemistry
Hamilton College, NY 13223

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