Dear Amber !
My aim is to calculate the energy between the solvent and solute !
regards
balaji
On Tue, Oct 19, 2010 at 12:52 PM, Sushil Mishra <sushilbioinfo.gmail.com>wrote:
> 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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> >
> >
> > --
> > 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 - 01:30:03 PDT
