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

From: David A Case <>
Date: Thu, 17 Sep 2020 08:58:08 -0400

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.


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Received on Thu Sep 17 2020 - 06:00:03 PDT
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