Re: [AMBER] solvation free energy

From: David A Case <>
Date: Tue, 22 Mar 2011 14:42:32 -0400

On Tue, Mar 22, 2011, Jorgen Simonsen wrote:
> I would like to calculate the solvation free energy of my protein
> complex which I have solvated in a periodic box which is neutral. I
> have seen in the documentation that it is possible to use the APBS
> module within amber but it seems that it is only using a GB model for
> the solvation or do I just plug in my solvated structure into the
> example(Amber 11)?

The APBS model would give a Poisson-Boltzmann estimate, not a GB one. You
could also do the same thing (much more easily) with Amber pbsa program.
In either case, you would have to strip the waters and counterions, giving
just the protein coordinates (not in a periodic box) to the program.

Note that the solvation energy per se won't give you much information: you
need to compare related strutures (e.g. with and without ligand, or with
alternate protein conformations) to learn something.

...hope this helps....dac

AMBER mailing list
Received on Tue Mar 22 2011 - 12:00:02 PDT
Custom Search