AMBER: AMBER vs QM: base pairing and stacking

From: Jiri Sponer <>
Date: Wed, 7 Dec 2005 19:22:02 +0100 (MET)

Hi everyone:

due to some recent uncertainties regarding
the reference (benchmark) QM data for force field,
and quality of AMBER,
I would like to clarify the following:

For H-bonding, the current reference values,
MP2 aug-cc-pVTZ -> aug-cc-pVQZ complete basis set (CBS) exptrapolation
and CCSD(T) correction
stand at
GC -29 kcal/mol
AT -15 kcal/mol

Accurate interaction energies of hydrogen-bonded nucleic acid base pairs
Sponer J., Jurecka P., Hobza P.
J Am. Chem. Soc. 126, 10142-10151, 18 2004

In this paper, AMBER is directly tested for dozens of base pairs
and except of the protonated one it works very well.

Cf. also:
Are the hydrogen bonds of RNA (AU) stronger than those of
DNA (AT)? A quantum mechanics study
Perez A., Sponer J., Jurecka P., Hobza P., Luque F.J., Orozco M.
Chem. Eur. J. 11, 5062-5066, 2005

Note also that the experiment by Yanson, Teplitsky and Sukhodub
cannot be compared with the force field, since any such
experiment rather inevitably includes a mixture of structures,
including stacks and may be T-shapes.
It anyway is enthalpy......

Global minimum of the adenine thymine base pair corresponds
neither to Watson-Crick nor to Hoogsteen structures.
Molecular dynamic/quenching/AMBER and ab initio beyond Hartree-Fock studies
Kratochvil M., Sponer J., Hobza P.
J. Am. Chem. Soc. 122, 3495-3499, 2000

AMBER also gives excellent values of ABSOLUTE stacking energies,
compared to our latest MP2/CBS + CCSD(T) data.
Relative values are reasonable, too,
although for testing we usually use MP2 charges.
There actually is an improvement compared to our benchmarks
from nineties.

Preliminary data:
Potential energy surface of the cytosine dimer:
MP2 complete basis set limit interaction energies,
CCSD(T) correction term, and comparison with the AMBER force field
Jurecka P., Sponer J., Hobza P.
J. Phys. Chem. B 108, 5466-5471, 2004
Full data:
Sponer et al,
Nature of base stacking. Reference quantum chemical
stacking energies in ten unique B-DNA base pair steps. Chem. Eur. J. in press

Finally, recent tests for functional RNA base pairing involving
the 2'OH are available and again show good AMBER performance,
so far for 2 classes of key RNA non-Watson-Crick families.

Non-Watson-Crick base pairing in RNA.
Quantum chemical analysis of the cis Watson-Crick/sugar edge base pair family
Sponer J.E.,et al.
J. Phys. Chem. A 109, 2292-2301, 2005

Principles of RNA base pairing: Structures and energies of
the trans Watson-Crick/sugar edge base pairs
Sponer J.E. et al.
J. Phys. Chem. B 109, 11399-11410, 2005

Geometries are available:
We put all geometries
as publicly available SI, so anyone can access them
and test any other force field readily.

The AMBER performance, considering its simplicity, is close to perfect.

best regards,

Jiri Sponer
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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Received on Wed Dec 07 2005 - 18:53:00 PST
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