This is a very interesting topic to discuss!
I would argue that the normal DNA staking may be just one possible case found in proteins...
Besides the "Sandwich" orientation, there are "Parallel-displaced" and "T-shaped" staking interactions among others...
https://doi.org/10.1021/ct800471b
I think those arrangements may be more difficult to represent with a standard FF... any comment is welcome...
On the other hand, the "zombie" pi-pi interactions seems to be statistically relevant in the PDB...
https://doi.org/10.7554/eLife.31486.001
All the best,
Matías
----- Mensaje original -----
De: "Jiri Sponer" <sponer.ncbr.muni.cz>
Para: "AMBER Mailing List" <amber.ambermd.org>
Enviados: Lunes, 10 de Mayo 2021 13:02:38
Asunto: Re: [AMBER] stacking interactions represented by force field equation?
I agree. In the first approximation, intrinsic stacking interactions
between two aromatic rings are suprisingly well described by the van der
Waals potential + point charge electrostatics.
So, there is no need for an explicit term for stacking interactions in the
ffs, it would just complicate.
Atom-centered point
charges provide enough flexibility for the electrostatic potential.
That means, the charges should reproduce reasonably well the ESP
of the monomers. As aromatic rings are rigid, the fixed charges work
well for all conformations. As AMBER force fields use ESP charges, they
are good for stacking,
which was the fundemental decision by P.A. Kollman long time ago.
The so-called "pi-pi effects" (something making aromatic stacking
special and different from "common" stacking and thus requiring
a specific force-field term) are in fact marginal.
These "zombie" effects are still popular in part of the literature but in
reality do not exist.
We have never detected them in rigorous QM calculations to be important,
despite that we have been trying to find them. Actually,
when we run the first electron correlation calcs on stacking around
~1995, we were looking forward to demonstrate how force fields
fail on stacking. Instead, we have got reasonable semiquantitative
agreement between QM and MM, which was a surprise for us.
One of the more recent reviews is
https://onlinelibrary.wiley.com/doi/abs/10.1002/bip.22322
older is
https://pubs.acs.org/doi/10.1021/cr9800255
What may be a concern in simulations is the balance with hydration, i.e.,
solvation energies, but this is not directly related to the description of
the intrinsic (direct) stacking interactions.
Best wishes, Jiri
n Mon, 10 May 2021, Carlos Simmerling wrote:
> Date: Mon, 10 May 2021 10:52:55 -0400
> From: Carlos Simmerling <carlos.simmerling.gmail.com>
> Reply-To: AMBER Mailing List <amber.ambermd.org>
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] stacking interactions represented by force field
> equation?
>
> this might be useful:
>
> https://pubs.acs.org/doi/10.1021/acs.jctc.8b00643
> Investigations of Stacked DNA Base-Pair Steps: Highly Accurate Stacking
> Interaction Energies, Energy Decomposition, and Many-Body Stacking Effects
> Holger Kruse*, Pavel Banáš, and Jiřı́ Šponer
> J. Chem. Theory Comput. 2019, 15, 1, 95–115
>
> On Mon, May 10, 2021 at 10:31 AM Martin Rosellen <
> martinrosellen.googlemail.com> wrote:
>
>> Dear Amber community,
>>
>> if I am right there is no explicit term for stacking interactions in
>> protein force fields such as ff14SB. I was wondering if force fields
>> somehow incorporate stacking interactions in the calculation of
>> non-covalent bonds?
>>
>> best
>> Martin
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Tue May 11 2021 - 09:00:03 PDT
