Re: [AMBER] Benzene Stacking in AMBER

From: Jiri Sponer <>
Date: Wed, 1 Dec 2010 11:40:31 +0100 (MET)

I entirely agree with what has been written
in all the earlier comments. Just small addition.
I assume base stacking is actually the best reproduced
term in AMBER simulations at least for NA.
The vdW term does reasonably well and the ESP charges as well.
As aromatic rings are rigid except of NH2, there is no problem with
using constant point charges (in contrast to all the flexible chains).
There are no so called "specific pi-pi effects" that would
make aromatic stacking somehow fundamentally different from
other simple molecular interactions, that we have shown around 1996.
Thus LJ vdW term + atom-centeried point charges are rather sufficient.
Specifically with benzene dimer, there could be a modest problem
if just 12 atomic charges can fully accurately describe its
quadrupole ESP distribution, which is responsible for
the T-shape and parallel displaced structure stabilization.
There also could be hidden problems with vdW term, some
attraction-repulsion imbalance.

Of course, I am far from telling ff is perfect.
We have done some more advanced analyses recently, such as
 Balance of Attraction and Repulsion in Nucleic-Acid Base Stacking: CCSD(T)/Complete-Basis-Set-Limit Calculations on Uracil Dimer and a Comparison with the Force-Field Description
 Author(s): Morgado CA, Jurecka P, Svozil D, et al.
 Source: JOURNAL OF CHEMICAL THEORY AND COMPUTATION Volume: 5 Issue: 6 Pages: 1524-1544 Published: JUN 2009

What I see as the main problem for studies (both theory and
experiment) of stacking and its role in the biomolecular complexes
is not the stacking description per se. The key issue is the complex
and system-specific
balance of forces in these systems. Often the free energy
trends do not reflect the "fundamental" forces such as stacking and
say base pairing, but the mixture of "everything else".
We did some comments for example in
 Nature and magnitude of aromatic stacking of nucleic acid bases
 Author(s): Sponer J, Riley KE, Hobza P
 Source: PHYSICAL CHEMISTRY CHEMICAL PHYSICS Volume: 10 Issue: 19 Pages: 2595-2610 Published: 2008

 Best wishes, Jiri

Jiri Sponer
Academy of Sciences of the Czech Republic
Kralovopolska 135
CZ-61265 Brno
Czech Republic
fax: 420 5412 12179
phone: 420 5415 17133

> > calculations. Interestingly for Benzene 'sandwiches' the AMBER force field
> > is actually pretty good, due mostly to the VDW parameters and the
> > electrostatic term. As opposed to PM3/PDDG which gives a totally repulsive
> Sponer/Hobza also have some very nice papers with nucleic acid base
> interactions that suggest that, despite the very simply MM model, the
> AMBER force fields (OPLS-like vdw + RESP derived charges) well reproduce
> high level QM...
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Received on Wed Dec 01 2010 - 03:00:02 PST
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