AMBER: Solvation free energy

From: Mike Wykes <>
Date: Mon, 19 Nov 2007 19:08:23 +0100

Dear all

I am not yet an Amber user, but am trying to find out if I can use Amber
to calculate the solvation free energy of a small molecule I am studying
in chloroform.

I read about MM_PBSA, thermodynamic integration using Sander and Amber
solvent models in the manual and have a few questions.

In the manual it says that chloroform is included in the solvent models.
Can I perform MD with my molecule in a box of explicit chloroform
molecules or is the chloroform represented by a continuum solvent model?
Or are both options possible?

If I want to use MM_PBSA to calculate the free energy of solvation, this
will only be possible with a continuum solvent approach.

Looking to the thermodynamic integration approach, I found this in the
AMBER Mail Reflector archive:

 To get the total solvation free energy, you would need to convert your
model compound to
 nothing in both the gas phase and in solvent, and then take the
 This would probably be done in two steps, one in which you remove all
of the charges, and
 a second in which you convert all atoms to dummy atoms.

I am wondering if this can be done with explicit solvent molecules
present (which gradually mutate as lamda goes from 0 to 1 ) or whether
this can only be done with an implicit solvent.

Many thanks

The AMBER Mail Reflector
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Received on Wed Nov 21 2007 - 06:07:25 PST
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