I think I will obtain that, after I perform certain task, like
minimization/equilibration/production, but what I want is to extract energy
of the post-processed structure, right after creating it(i.e., right after
solvating and adding counter-ions to my main protein system)?
On Tue, Apr 9, 2019 at 6:06 PM Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> Yes these are saved to the mdout file at a frequency set by the input
> variable ntpr.
>
> On Tue, Apr 9, 2019, 8:32 AM Akshay Prabhakant <akshayresearch16.gmail.com
> >
> wrote:
>
> > I apologise for incorrectly framing the question. What I wanted to ask
> was,
> > just as we can use the NAMDEnergy plugin in vmd to find various energies
> of
> > the system under consideration(bond energy, vdw, elec, dihedral etc.), is
> > there any tool in amber md to do the exact same task?
> >
> >
> > On Tue, Apr 9, 2019 at 5:18 PM Carlos Simmerling <
> > carlos.simmerling.gmail.com> wrote:
> >
> > > Zero point energies don't have any meaning in molecular mechanics. The
> > zero
> > > is arbitrary. Only energy differences should be interpreted (relative
> > > energies of different conformations, or of bound and unbound states).
> > >
> > > On Tue, Apr 9, 2019, 7:43 AM Akshay Prabhakant <
> > akshayresearch16.gmail.com
> > > >
> > > wrote:
> > >
> > > > Hello everyone,
> > > > I have a protein system, and would like to calculate its zero point
> > > > energies(bond energy, vdw energy, electrostatic-interaction energy
> > > etc.). I
> > > > have gone throigh the "mmpbsa" method, but dont seem to understand
> how
> > to
> > > > apply it for just a protein system(no ligand involved, just the
> > protein).
> > > > Can somebody tell me a way of going about my task? Thanks in
> advance.
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Received on Tue Apr 09 2019 - 06:00:05 PDT
