Re: [AMBER] Calculate zero point energy for a protein (no ligand) system

From: MOHD HOMAIDUR RAHMAN <rahmanhpu.gmail.com>
Date: Wed, 10 Apr 2019 00:19:17 +0530

Hi Prabhakant,
ambertool also have similar modules like NAMDEnergy pluging. See amber 18
manual for more details, as mention below,
1) page no 643; energy
2) page no 644; esander
2) page no 321; imin=5
3) page no 671; pairwise
4) page no 739; MMPBSA example
thanks
HTH
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*M*d* H*omaidur* R**ahman *( Research Scholar )
Lab No. 510, Computational Biophysics Lab.
Department of Biotechnology
Indian Institute of Technology-Madras
Chennai-600 036, India
*Mobile No = +91- 7845991785*
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On Tue, Apr 9, 2019 at 6:17 PM Akshay Prabhakant <akshayresearch16.gmail.com>
wrote:

> 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 - 12:00:02 PDT
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