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 - 06:00:03 PDT
