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

From: Adrian Roitberg <>
Date: Thu, 17 Sep 2020 13:20:47 -0400

Look at the flag imin=5 in sander that can take for example a trajectory
and compute single point energies for every frame.

This is what you would want to use for your case.

In reality, for Marcus theory, you need the free energy difference to
redox state at a given geometry. As such, just recomputing single point
energies (let's say you ran the reduced state and do single point in the
oxidized state) is not enough, and you would need something like free
energy perturbation or TI calculation.

If your system is 'big', which I assign as larger than > 100 atoms
maybe, then the inherent fluctuations in potential energy at a given T
are large, which means trying to nail down energy differences is very hard.

I think cpptraj also has its own single energy calculator.

One very non-trivial point: When you use Ewald sums, there is a
correction to the total energy due to the fact that your central box
might not be charge-neutral. This is not a 'huge' deal, but one needs to
be careful, and Amber has a good automatic solution for this.

However, we you change charge form reduced to oxidized, you need to be
VERY careful with that. I honestly do not know how to do it well, but I
can see one needs to figure it out.


On 9/17/20 1:07 PM, Vaibhav Dixit wrote:
> [External Email]
> 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
> this?
> 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
> default?
> 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
> possible/available.
> 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
> Vaibhav
> 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
> --
> Regards,
> Dr. Vaibhav A. Dixit,
> Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
> University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
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> Phone No. +91 1596 255652, Mob. No. +91-7709129400,
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Dr. Adrian E. Roitberg
V.T. and Louise Jackson Professor in Chemistry
Department of Chemistry
University of Florida
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Received on Thu Sep 17 2020 - 10:30:03 PDT
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