Thank you Jason, I donīt have a copy of Amber package, hence I donīt have
access to the source code, I will ask some friends if they could send me the
file mdread.f
Osvaldo Martin
On Tue, May 10, 2011 at 11:52 AM, Jason Swails <jason.swails.gmail.com>wrote:
> These are found in the sander source code (mdread.f).
>
> On Tue, May 10, 2011 at 4:10 PM, Osvaldo Martin <aloctavodia.gmail.com
> >wrote:
>
> > Hello everybody,
> >
> > 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 am using the Amber99 forcefield, I trying downloading a parameter file
> > from the Amber web page but I could not found the surface parameters per
> > atom type inside. BTW, I also found this paper "Approximate Atomic
> Surfaces
> > from Linear Combinations of Pairwise Overlaps" this paper have parameters
> > to
> > calculate the surface area, but i need the parameters to "translate" the
> > surface area into energy.
> >
> > thanks in advance.
> >
> > Osvaldo Martin
> >
> > <http://www.sanluis-conicet.gob.ar/imasl/>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue May 10 2011 - 08:30:03 PDT
