Re: [AMBER] pi-pi And Aromatic Interactions

From: Christina Bergonzo <>
Date: Fri, 19 Oct 2018 08:49:58 -0400


I wanted to give a more nuanced look at the pi-pi and cation-pi interaction
in MD force fields.

While there is no explicit force field term for pi-pi or cation-pi
interactions, you can of course look for their effects, which are indeed
represented using MD - otherwise my DNA duplexes would be in trouble!
Force fields rely on van der Waals to pick up the effects of these
interactions, and generally they can capture those effects - of course,
this is modulated by the desired level of accuracy.

You can take a look at these papers to get an understanding of the issue
w.r.t. QM:

Here is an example where we measured base eversion pathways, noted a
cation-pi interaction, and experimental collaborators made the mutation to
disrupt it, causing catalytic activity of the protein with an (aromatic)
damaged DNA base to decrease, but leaving the activity of the
(non-aromatic) apurinic damage intact:

And here is an example of base stacking in RNA, where it is argued that
pi-pi stacking is overstabilized:

For analysis of these types of interactions, I would make sure to look at
not only the energies but also the distances and geometries of pi-pi or
cation-pi binding pairs.

Hope this helps,

On Thu, Oct 18, 2018 at 11:27 PM Chris Neale <> wrote:

> Be careful... atomistic force fields typically don't have any pi electron
> effects in the Hamiltonian, so why would you analyze for them? In fact,
> most atomistic force fields do a pretty terrible job at pi-based effects
> like aromatic stacking. Same goes for cation-pi interactions.
> On Thu, Oct 18, 2018 at 8:08 PM Meng Wu <>
> wrote:
> > Dear all,
> >
> > I have MD for my channel protein and substrate molecules and I have
> > used the "lie" command to calculate the EELEC and EVDW terms. Now I want
> to
> > analysis like the pi-pi interactions or aromatic interactions between the
> > substrates and protein & residue to residue in protein, could anybody
> give
> > me some suggestions? Thank you in advance!
> >
> > Best regards,
> > Meng Wu
> >
> > _______________________________________________
> > AMBER mailing list
> >
> >
> >
> _______________________________________________
> AMBER mailing list

Christina Bergonzo
Research Chemist
NIST/IBBR NRC Postdoctoral Researcher
AMBER mailing list
Received on Fri Oct 19 2018 - 06:00:04 PDT
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