My Interest is to extract ligand surrounding energies (vdW and el) from
explicit solvent MD simulation. I would like to try LIE (from
those surrounding energies ) for calculation of binding fee energies.
On Tue, Oct 19, 2010 at 10:32 AM, Daniel Sindhikara <sindhikara.gmail.com>wrote:
> 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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> > >
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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 Tue Oct 19 2010 - 00:30:04 PDT
