Re: [AMBER] solvation free energy

From: David A Case <>
Date: Tue, 14 Oct 2014 08:27:23 -0400

On Tue, Oct 14, 2014, kirtana S wrote:

> As I understand to calculate the solvation energy I have to use PBSA to
> calculate the polar solvation energy. To estimate the non-polar part of
> solvation energy I have to use SASA + Vander Waals interaction energy
> between solute and solvent atoms.
> My question is about the type of files I will use to calculate this, i.e
> the prmtop and inpcrd file. Do I need to solvate it or use continuum
> solvent model.

You just want to use the PBSA program: see Chap. 5 of the Reference Manual.
PBSA is a form of continuum solvent model.

I am still concerned that you are using terms like "accuracy" for your
problem (estimating the solvation free energy of a solute with 5000
atoms). You can use pbsa to compute this number, but neither you nor
anyone else will have any idea of its accuracy, and you should be prepared
for the result to be, in fact, wildly innaccurate.


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Received on Tue Oct 14 2014 - 05:30:03 PDT
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