[gmx-users] Pi Stacking in OPLSAA ff

David van der Spoel spoel at xray.bmc.uu.se
Thu Jan 10 11:05:16 CET 2008

Ramya Cherukupalli wrote:
> Dear all,
>     I am trying to simulate a mutant lipase molecule using OPLS AA
> forcefield. In the crystal structure study, presence of a Pi-stacking
> interaction has been proposed to help in enhancement of thermostable
> behavior of the mutant.
> I wanted to clarify 2 things..
> 1. Does OPLS AA parameterize/recognize Pi-stacking?? Actually i do have
> read some papers  which dealt with pi-stacking using OPLS ff but nothing
> is mentioned whether we have to declare pi-stacking as a *patch* for the
> ff to identify.. or not????
This is not explicitly modeled. It comes in through 
qaudropole-quadrupole interactions, but these compete with packing 
(sterical effects) and Van der Waals interactions. You can probably find 
some older literature on it, like this one:

         author = {William L. Jorgensen and Daniel L. Severance},
         title = {Aromatic-Aromatic Interactions: Free Energy Profiles 
for the Be
         Dimer in Water, Chloroform and Liquid Benzene},
         journal = BTjacs,
         year = {1990},
         volume = {112},
         pages = {4768--4774},


and for amber:

         author = {C. Chipot and R. Jaffe and B. Maigret and D. A. 
Pearlman and P
. A.
         title = {Benzene dimer: A good model for {$\Pi-\Pi$} 
interactions in Pro
         A comparison between the benzene and toluene dimers in the gas 
         and in aqueous solution},
         journal = BTjacs,
         year = {1996},
         volume = {118},
         pages = {11217-11224},


> 2. I am not sure about the process of creating a *patch* in Gromacs.. So,
> can anyone help me out for the same.. ????
>       If anyone has worked in this earlier, suggestions are welcome..
> Thank you in advance,
> Regards,
> -----------------------
> Ramya Cherukupalli,
> M.S (by Research) Bioinformatics,
> IIIT - H.
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David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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