Aromatic base stacking and similar interactions are very
well described by ESP charges + reasonable vdW term.
Nature of base stacking: Reference quantum-chemical stacking energies in ten unique B-DNA base-pair steps
Author(s): Sponer J, Jurecka P, Marchan I, Luque FJ, Orozco M, Hobza P
Source: CHEMISTRY-A EUROPEAN JOURNAL 12 (10): 2854-2865 MAR 20 2006
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
Author(s): Jurecka P, Sponer J, Hobza P
Source: JOURNAL OF PHYSICAL CHEMISTRY B 108 (17): 5466-5471 APR 29 2004
etc .. etc..
The original reference with the above statement is:
Nature of nucleic acid-base stacking: Nonempirical ab initio and empirical potential characterization of 10 stacked base dimers. Comparison of stacked and H-bonded base pairs
Author(s): Sponer J, Leszczynski J, Hobza P
Source: JOURNAL OF PHYSICAL CHEMISTRY 100 (13): 5590-5596 MAR 28 1996
Pi charges were (without much effect) tested in:
Base stacking in cytosine dimer. A comparison of correlated ab initio calculations with three empirical potential models and density functional theory calculations
Author(s): Sponer J, Leszczynski J, Hobza P
Source: JOURNAL OF COMPUTATIONAL CHEMISTRY 17 (7): 841-850 MAY 1996
Jiri Sponer
[ Charset ISO-8859-1 unsupported, converting... ]
> Dear all:
>
> are the Amber force fields suitable to this kind of interaction (pi-pi)?
>
> []s,
>
> Roberto
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed May 23 2007 - 06:07:24 PDT
