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????
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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