Hello,
This specific problem I can see a possible solution, though please someone
step in if I'm missing something obvious. You can decompose the energy of
this system into 5 components:
E tot = E int,solvent + E int,solute + E nb,solute->solute + E
nb,solvent->solvent + E nb,solute->solvent, where the terms are the internal
potential terms (angle, bond, dihedral, 1-4s) for the solvent and solute,
and then the non-bonded terms between solute atoms, nonbonded terms between
solute atoms, and then, what you're finally looking for, the nonbonded terms
between the solute and solvent (I don't think I'm missing any terms here).
What you have to do is find a way of isolating the last term. The total
energy is going to be the sum of all, so if you can isolate the first 4 and
subtract them from the total, you'll get what you're looking for.
What you'll need: leap to create prmtop files, ptraj and the strip command,
sander with the imin=5 option. These are described thoroughly in the
manual, and I will not detail further how to implement this plan.
1. Strip the solvent from the original trajectory file and create a matching
prmtop file (check that they actually match with a visualization program!)
2. Strip the solute from the original trajectory file and create a matching
prmtop file (again, check that they match)
3. Use sander and imin=5 (with maxcyc=1 to just extract energies) to get the
energy for each frame for each trajectory. The stripped solvent should give
you E int,solute + E int,solute->solute. The stripped solute trajectory
should give you E int,solvent + E int,solvent->solvent. Thus, if you
subtract these 2 values from the total, all you'll be left with is E
nb,solute->solvent.
This may be tedious to implement, but it is relatively straightforward and
should help increase your familiarity with amber and its various tools.
Hope this helps,
Jason
On Tue, Oct 19, 2010 at 4:11 AM, lara lara <lara.4884.gmail.com> wrote:
> 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
> > > > >
> > > > >
> > > > > _______________________________________________
> > > > > AMBER mailing list
> > > > > AMBER.ambermd.org
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > >
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > >
> > >
> > >
> > > --
> > > Dr. Daniel J. Sindhikara
> > > Institute for Molecular Science
> > > E-mail: sindhikara.gmail.com
> > > Website: http://sites.google.com/site/dansindhikara/
> > > --
> > > _______________________________________________
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> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
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> >
> _______________________________________________
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Tue Oct 19 2010 - 08:00:04 PDT
