On Tue, May 10, 2011, Osvaldo Martin wrote:
>
> I am trying to implement a routine (I need it to use it outside the Amber
> package) to estimate the solvatation energy of proteins using the Solvent
> Accesible Surface Area approach. i.e
>
> G_solv ~= sum (surface area per atom type * surface parameter per atom type)
I don't think(?) that Amber uses this equation: we calculate the surface area
using the LCPO approximation, as in the paper you cite, but use a single
"surface tension" for all atom types. This is an estimate of the *non-polar*
contribution to solvation, not an approximation to the total solvation free
energy.
As is often the case, people stick things into Amber that I don't know about,
so there may be something I am missing here. If so, I rely on Adrian to
provide the correction....
....dac
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Received on Tue May 10 2011 - 10:00:02 PDT
