[gmx-users] Re: help about topol.tpr file of small molecular complex

[Ing. Vojtěch Spiwok]

Hi
I think one can get reasonable MD results without going to quantum
chemistry. The paper from PNAS abot pi-cation interactions (I expect
this is the study of this phenomenon) shows good correlation between
force-field energy and HF/6-31G** energy for such interactions taken
from known protein structures. In MM calculations these interactions
are treated as electrostatic interactions between cation and negatlively
charged carbon atoms of aromatic ring. Such interaction energies are
underestimated.
http://www.pnas.org/cgi/content/full/96/17/9459
Cation-pi interactions in structural biology 
Justin P. Gallivan and Dennis A. Dougherty
Vol. 96, Issue 17, 9459-9464, August 17, 1999

Cheers
Vojtech Spiwok