There is no pi-pi stacking potential term included in any force field that
Amber uses. These effects would be captured in the VDW potential term, most
likely, which is the best you could do. You could do pairwise decomposition
with MMPBSA.py and look at the vdw term between the two stacking residues
(being sure to use the decomp method that puts 1-4 VDW into the internal
contribution).
The best that will give you, though, is the total van der Waals interaction
between the two residues, which is not easily decomposable into a "pi-pi
stacking" and other terms.
Hope this helps,
Jason
On Thu, Mar 17, 2011 at 8:05 AM, John S <s.john634.gmail.com> wrote:
> Dear Amber Users,
>
> I need to measure the pi pi stacking interaction energy .Which is the best
> method to do so.
>
> Thanks
> John
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Mar 17 2011 - 09:00:03 PDT
