AMBER Archive (2009)

Subject: Re: [AMBER] calculation of Pi-Pi interaction energy

From: Jiri Sponer (
Date: Wed Apr 01 2009 - 07:38:49 CDT

Pi-Pi forces are quite well described by the force field.
In contrast, semiempirical methods and most of the DFTs fail
notoriously for dispersion.
Base stacking is the best reproduced force in DNA or RNA simulations
with AMBER.

Few refs:
J.Sponer, K. E. Riley, P. Hobza: Nature and magnitude of aromatic stacking of nucleic acid bases. Physical Chemistry Chemical Physics 10, 2008, 2595-2610

J. Sponer, P. Jurecka, P Hobza: Base stacking and base pairing. In: Computational studies of RNA and DNA. J. Sponer, F. Lankas, Eds., Computational studies of RNA and DNA. Dordrecht: Springer, 2006, pp. 343-388

J. Sponer, P. Jurecka, I. Marchan, F. J. Luque, M. Orozco, P. Hobza: Nature of base stacking. Reference quantum chemical stacking energies in ten unique B-DNA base pair steps. Chemistry - A European Journal 12, 2006, 2854-2865

P. Hobza, M. Kabelac, J. Sponer, P. Mejzlik, J. Vondrasek: Performance of empirical potentials (AMBER, CFF95, CVFF, CHARMM, OPLS, POLTEV), semiempirical quantum chemical methods (AM1, MNDO/M, PM3) and ab initio Hartree-Fock method for interaction of DNA bases. Comparison with nonempirical beyond-Hartree-Fock results. Journal of Computational Chemistry 18, 1997, 1136-1150

J. Sponer, J. Leszczynski, P. Hobza: On the nature of nucleic acid base stacking. Nonempirical ab initio and empirical potential characterization of 10 stacked base pairs. Comparison of stacked and H-bonded base pairs. Journal of Physical Chemistry 100, 1996, 5590-5596

For amino acids is the same, reasonable vdW Lennard Jones term + ESP electrostatics
are OK for so called "pi-pi" stacking, unless you have 20 or more atoms in the
fused rings, this leads to some orbiral pipi effects, but
is not the case of biopolymers.

Best wishes Jiri

Jiri Sponer
Professor of Biochemistry
Head of Department of Structure and Dynamics of Nucleic Acids
Institute of Biophysics
Academy of Sciences of the Czech Republic
Kralovopolska 135
CZ-61265 Brno
Czech Republic
fax: 420 5412 12179
phone: 420 5415 17133

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> Dear Aneesh
> in my opinion using MM is not the best choice to extimate the p-p
> interaction, i would use something Quantum.
> In Amber there are some semiempirical methods, maybe you can use one of
> these, but preliminary you need to evaluate the best methods for p-p
> interaction.
> To extimate the p-p interactions maybe you can do something like alanine
> scanning, you can do this using MM (or also QM, in this case you can use
> simple models of the binding site).
> Good luck
> Jacopo
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