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:
@article{Jorgensen90,
author = {William L. Jorgensen and Daniel L. Severance},
title = {Aromatic-Aromatic Interactions: Free Energy Profiles
for the Be
nzene
Dimer in Water, Chloroform and Liquid Benzene},
journal = BTjacs,
year = {1990},
volume = {112},
pages = {4768--4774},
}
and for amber:
@article{Chipot96a,
author = {C. Chipot and R. Jaffe and B. Maigret and D. A.
Pearlman and P
. A.
Kollman},
title = {Benzene dimer: A good model for {$\Pi-\Pi$}
interactions in Pro
teins?
A comparison between the benzene and toluene dimers in the gas
phase
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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Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
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