Re: AMBER: Solvation free energy

From: Thomas Steinbrecher <steinbrt.scripps.edu>
Date: Mon, 19 Nov 2007 10:21:23 -0800 (PST)

Hi Mike,

regarding the use of thermodynamic integration to calculate the solvation
free energy of a small molecule, yes that can be done in explicit solvent
and this would be the standard approach to do it.

You would have to set up a box with your molecule of choice embedded in
chloroform solvent (amber's leap programm comes with a premade CHCL3BOX
that makes this easy). One of the tutorials on the amber webpage on TI
will be helpful there.

It is probably possible to do TI with implicit solvent, but for a small
molecule, the computational ressources needed to do the calculation will
be moderate, so doing all necessary TI steps with full explicit solvent is
usually not a problem.

Kind Regards,

Thomas

Dr. Thomas Steinbrecher
The Scripps Research Institute
10550 N. Torrey Pines Rd.
San Diego CA 92037, USA
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Received on Wed Nov 21 2007 - 06:07:25 PST
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