Not sure how much I can help here, but to start, you can tell us
how you are treating the solvent. Explicit? PB, GB?
As for hydration free energies, it's quite simple to do in TI (with explicit
solvent) in
AMBER. But it looks like Balaji is looking for the instantaneous interaction
potential.
--Dan
On Tue, Oct 19, 2010 at 1:03 PM, Sushil Mishra <sushilbioinfo.gmail.com>wrote:
> Hi,
>
> I am also interested in this question. Usually this is needed for FEP
> calculations but unfortunately we dont have FEP implemented in amber. I
> will
> ask about thermodynamic integration. When we do TI calculation, then can we
> write interaction energy of ligand from its surrounding. I would
> be interested to use amber for using Linear interaction energy approach for
> free energy calculation. What i need from the AMBER simulation is, vdW
> and electrostatic interaction energy of particular group of atoms (for
> whole
> ligannd and may be some ions) in salivated protein ligand complex.
>
> Please can anyone suggest the way to extract interaction energies in amber
> ?
>
> ..Sushil
>
>
> On Tue, Oct 19, 2010 at 8:43 AM, balaji nagarajan
> <balaji_sethu.hotmail.com>wrote:
>
> >
> > dear Amber 1
> >
> > I would like to know the interaction between the solvent and the
> > solute is it possible to do in amber ?
> >
> > The Energy printed in amber is for the total , but i would like to know
> the
> > interaction energies , how one can do this with amber ?
> >
> > regards
> > balaji
> >
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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>
--
Dr. Daniel J. Sindhikara
Institute for Molecular Science
E-mail: sindhikara.gmail.com
Website: http://sites.google.com/site/dansindhikara/
--
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Received on Mon Oct 18 2010 - 22:30:03 PDT
