Hi Osvaldo,
Sorry, it should also be in the NAB source code, since NAB can do LCPO as
well. I think cpptraj also has it with AmberTools 1.5.
All the best,
Jason
On Tue, May 10, 2011 at 5:22 PM, Osvaldo Martin <aloctavodia.gmail.com>wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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> 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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Received on Tue May 10 2011 - 09:00:02 PDT
