Re: [AMBER] expected average fluctuations in amino acid covalent bond distances, angle and torsion during typical md simulations

From: Vaibhav Dixit <>
Date: Thu, 17 Sep 2020 22:37:44 +0530

Dear David and AMBER community,
In analogy with the JACS paper, I will get inner-sphere reorg.Es from a QM
calculation of a small-model/active site model.
And as you mentioned I can use the MD simulations for the outer-sphere and
long-range effect on reorg.Es
But I have the following technical Amber specific query in this regard.
How to estimate the force-field based Es for reduced-state in the
oxidized-state geometry and vice-versa?
One tedious (and probably worst) method I can imagine is to save pdb for
each snapshot of the oxidized trajectory and then create new prmtop/inpcrd
files using parameters for reduced-state and then, I don't know how to, get
only force-field based Es without minimizing the protein. Can cpptraj do

Do we have some sort of a smarter direct option (in cpptraj or other
AmberTools) to read coordinates from Amber MD trajectories and calculate
only Es with options to chose/change FF parameters (standard/non-standard)
without minimizing the structure? That is what are the options to perform
single-point calculations on protein structure, as many QM programs have by

Is it possible that the prmtop file for the reduced state will work with
mdcrd file for the oxidized state, since the two states are expected to
have same topology and connectivity (no covalent bonds are breaking/forming
during the electron transfer)? I think this would be the best option if

Yes, I can't agree more, molecules are molecules and so I understand that
the same procedure should work for proteins IR-spectra (with known
limitations for the method).
Thank you very much for your valuable/insightful comments/suggestions.
Best regards

On Thu, Sep 17, 2020 at 6:28 PM David A Case <> wrote:

> On Wed, Sep 16, 2020, Vaibhav Dixit wrote:
> >Moving one step forward with your response is it then possible to estimate
> >Marcus parameters e.g. reorganization energies from MD simulations for
> >protein redox states with MD simulations using Amber/AmberTools?
> It depends on the accuracy/precision that you need, and on the type of
> system. Reorganization energies are often dominated by long-range
> electrostatic interctions that are reasonably well-described by force
> fields. But a complete study would indeed require one to look at
> "inner-sphere" changes right around the place where the electron
> transfer occurs. As you already know, some sort of quantum study would
> then be required.
> In the abstract of the paper you cite, the dominant factor in the
> reorganization energy is the response of solvent and collective modes of
> the protein.
> >Also, if I understood correctly, the cellulose IR spectra example a
> >non-protein system and thus doesn't address my query about IR spectra of
> >proteins from MD simulations.
> Molecules are molecules, are they not? The computational procedures
> involved would be the same for proteins.
> ....dac
> _______________________________________________
> AMBER mailing list

Dr. Vaibhav A. Dixit,
Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
Assistant Professor,
Department of Pharmacy,
Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
Phone No. +91 1596 255652, Mob. No. +91-7709129400,
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Received on Thu Sep 17 2020 - 10:30:02 PDT
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