I have read a lot on this subject since I wanted to prove one such interaction 
myself (between inhibitor and enzyme).

Generally, authors who talk of such interaction never give proof using 
simulation, but use a simple geometric criteria (benzene rings are superposed 
in T-shape or face-to-face staggered configuration at a given distance) to 
describe them in crystal structures.

For modeling, there are a few papers (beginning 1990s, not quite recent) which 
used a point charge model to model pi-pi stacking (Hunter-Saunders model). In 
this model, charges are distributed onto the hydrogens and in the middle of the 
benzene ring (with a dummy atom) and their results (geometry optimization) 
showed some similarity to experimental results seen in crystals. I can give you 
the references if you like.

However, pi-pi interactions have some polarization component, and so they have 
been best modeled with quantum mechanics; this would involve doing a QMMM 
simulation. I have not seen yet a paper talking about QMMM simulation of pi-pi 
stacking (if somebody has seen one please give me the reference)

I have also heard of polarizable force fields, but I don't know if they can 
model pi-stacking properly.

If somebody has heard of a proven method of modeling pi-stacking, energy- and 
geometry-wise, I would also be very interested in it.

Diane

   


-----Original Message-----
From: [EMAIL PROTECTED] on behalf of Wei Fu
Sent: Wed 7/26/2006 11:44 AM
To: gmx-users@gromacs.org
Subject: [gmx-users] does gromos force field can explain pi-pi interaction
 
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
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!

Linda


_______________________________________________
gmx-users mailing list    gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

<<winmail.dat>>

_______________________________________________
gmx-users mailing list    gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Reply via email to