[gmx-users] does gromos force field can explain pi-pi interaction
David van der Spoel
spoel at xray.bmc.uu.se
Wed Jul 26 19:28:14 CEST 2006
Wei Fu wrote:
> Dear gmx users,
> My simulation shows that the aromatic ring of ligand forms stacking
> pi-pi interaction with the side chain of Phe of receptor during MD
> One reviewer of my manuscript questions that such pi-pi interaction can
> not accurately accounted for by the employed force field.
> I do not know how to answer this question, any idea is highly appreciated!
which gromos force field did you use?
the recent ones (96+) have explicit hydrogens on the sidechains and
hence they can form these quadrupolr interactions. You can probably not
claim quantitative accuracy and unfortunately I don't think there is any
objective test of this feature of the force field.
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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