Dear David, Adrian and Amber community,
Thanks for highlighting the imin=5 options for sp calculation.
There seems be an mmpbsa_py_energy option that give sp Es, but that would
strip the waters and give protein Es in a solvent (GB/PB) model.
Is this also true for the imin=5 option which seems to be used with irism
keword in the manual?
On page 105 (Amber20 manual) it says that RISM is different from explicit
and implicit models.
imin=5 appears only 7 times in the manual, thus I'm not sure what are the
inherent assumptions and I'm not aware of the RISM method either.
Can you please help me understand if this approach "Trajectory
Post-Processing (imin=5)" can give me the FF-sp-Es for a structure of
choice from the trajectory without removing waters and without solvent
models?
I agree with your comment about requirement of "Free Energies" for Marcus
parameters, but the authors of the JACS, 2010, 132, 47, 17032–17040
<
https://doi.org/10.1021/ja107876p> haven't explicitly mentioned using TI
or other methods, but are claiming to estimate "free energies" thus I'm
assuming that they are calling FF-sp-Es as "free energies". If this is
wrong, would that make their results less reliable? Is it valid because of
the "limit of linear response" that they mention for outer-sphere reog.Es.
Also the Figure 4-panel-D, red curve is unexpectedly smooth, I don't
understand why/how? There is nothing in the SI that can help answer some
of these questions. The used Amber9, thus I was hoping that progress since
then would have made such calculations more feasible/streamlined.
Please let me know how would you approach this problem for getting the
reorg.E or are they too difficult to estimate with current state-of-the-art
software/hardware and theory?
Thank you very much for your time and expert comments/suggestions on these
aspects.
Best regards
On Thu, Sep 17, 2020 at 10:52 PM Adrian Roitberg <roitberg.ufl.edu> wrote:
> 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.
>
> adrian
>
>
> 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 <david.case.rutgers.edu>
> 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
> >>
> >> _______________________________________________
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> >>
> >
> > --
> >
> > 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.
> > AND
> > Assistant Professor,
> > Department of Pharmacy,
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> > Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
> > VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
> > India.
> > Phone No. +91 1596 255652, Mob. No. +91-7709129400,
> > Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
> >
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> --
> Dr. Adrian E. Roitberg
> V.T. and Louise Jackson Professor in Chemistry
> Department of Chemistry
> University of Florida
> roitberg.ufl.edu
> 352-392-6972
>
>
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--
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.
AND
Assistant Professor,
Department of Pharmacy,
▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
India.
Phone No. +91 1596 255652, Mob. No. +91-7709129400,
Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
ORCID ID: https://orcid.org/0000-0003-4015-2941
http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
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Received on Fri Sep 18 2020 - 02:30:02 PDT
