AMBER: implicit solvent free energy calcs

From: David Mobley <>
Date: Thu, 15 Feb 2007 10:07:37 -0800

Dear all,

I'm considering doing free energy calculations in implicit solvent,
and was curious whether anyone has done anything along these lines in
AMBER. Are you aware of any work along these lines?

Is there any reason to think that the current free energy code would
*not* work properly for this? Particularly, I'm thinking of changing
or removing charges on a small molecule in the context of, say,
hydration free energies. When it comes to the nonpolar component, I'm
assuming that I'd actually have to modify the GB parameters for
specific atom types in order to turn off the nonpolar interactions
with the environment, or is there an easier way to do this?

Thanks a lot,
David Mobley
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Received on Sun Feb 18 2007 - 06:07:22 PST
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