David I think you are probably right, and I am probably mixing things. I
should think this more carefully.
Thanks,
On Tue, May 10, 2011 at 1:41 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> 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 - 10:00:04 PDT
