Re: [AMBER] solvation free energy

From: David A Case <>
Date: Sun, 12 Oct 2014 08:38:04 -0400

On Sun, Oct 12, 2014, kirtana S wrote:
> I want to calculate the solvation free energy of my solute which consists
> of 5000 atoms. My solute is already solvated in explicit solvent. If I use
> MMPBSA ,do I need to have three separate systems i.e solvent, solute and
> solvated solute. Only after I obtain the change in free energy from all the
> three states I can calculate the electrostatic contribution to solvation
> energy. Here how can I obtain the hydrophobic contribution.
> Is there any other method to obtain the solvation free energy.

First, are you sure this is what you want to estimate? There are no
measurements of such numbers, and not a lot you can do with the value you
would obtain.

MM/PBSA does not handle the sort of calculation you have in mind. You could
get a quick estimate of the solvation free energy by carrying out a PB
calculation; (if the molecule is floppy, you probably need to average results
over a set of representative solute conformations).

I don't immediately see a good way to use explicit solvent to do this.

Maybe if you tell us what you hope to do with this information, people could
suggest some alternate approaches.


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Received on Sun Oct 12 2014 - 06:00:03 PDT
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