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
field.
I do not know how to answer this question, any idea is
highly appreciated!
None of the MM force field can reproduce pi-pi
interactions
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.
XAvier
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