[gmx-users] does gromos force field can explain pi-pi interaction

X.Periole X.Periole at rug.nl
Thu Jul 27 10:09:17 CEST 2006

>    My simulation shows that the aromatic ring of ligand 
>forms stacking
> pi-pi interaction with the side chain of Phe of receptor 
>during MD
> simulation.
> One reviewer of my manuscript questions that such pi-pi 
>interaction can
> not accurately accounted for by the employed force 
> I do not know how to answer this question, any idea is 
>highly appreciated!

None of the MM force field can reproduce pi-pi 
for the simple reason that the force field does not
describe electrons explicitly !! That is the case for
most of the interactions involving electrons !! The same
for H-bonds. At the time of FF development their were
a big problem !! Not transfert of electrons in MM !!
Basically a FF sucks when a chemist looks at it !!

On the other hand the MM-FF have been parametrized to
reproduce average properties of small compounds (see the
GROMOS FF description) and several type of funny 
interactions can be observed. In the GROMOS FF the C in
the rings in PHE and TYR have partial charges to reproduce
the delocalization of the electrons ... as a comparison
the C of the LYS side chain do not have any partial
charges !!

What you see is not a pi-pi stacking interaction but an
"interaction between two rings that could be assimilated
to a pi-pi interaction although you do not have explicit
description of electrons or polarization". There different
ways to say things !! Saying you have pi-pi stacking is
definitely too much.


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