AMBER: MM_PBSA parameters

From: Nelson Fonseca <>
Date: Tue, 06 Dec 2005 15:26:55 +0000

Nelson Fonseca <>
Dear Amber users:
Our group is interested on the study of the binding interactions between
ligands and receptors. These studies are carried by molecular dynamics
in a wide range of organics solvents  such as DMSO, methanol, CCl4 and
ethanol. For the estimative of the binding energy associated with the
bindng recognition process we are interested to use pos-processing
methods such as MM-PBSA analysis. However on the best of our knowledge
parameters for the non-polar contribution (Gnp) for  these solvents
(dmso,methanol, ethanol and CCl4)  are not available from the
literature.  We would like to know if it is possible to apply the
mm-pbsa methodoly to the simulations performed  with these solvents. In
other words there are parameters available for these solvents in order
to use the sripts  type provided with amber 8.
Thanks in advance,
Nelson Fonseca
Department of Chemistry
University of Aveiro

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Received on Tue Dec 06 2005 - 15:53:00 PST
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