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 - 06:00:04 PDT
