[gmx-users] Empirical potential for Pi stacking interactions?

Delmotte, Antoine antoine.delmotte09 at imperial.ac.uk
Fri Aug 10 11:12:27 CEST 2012

Dear Gromacs users,

I am currently looking for an empirical potential for pi stacking 
interactions. Something like the Leonard Jones potential, or the Mayo 
potential for hydrogen bonds. I was wondering if something like that 
exists for pi stacking interactions?

I am not really looking for something that would be super accurate, I am 
mainly looking for an expression which would give me a good enough 
approximation of the pi stacking interaction energy, even if it is a 
relatively crude approximation, in the case of DNA bases in particular.

Basically, something I could calculate relatively easily from the 
coordinates of the bases directly, without having to run my PDB file 
through a full MD package.

I know that this is not a question directly related to Gromacs, but this 
mailing list seems to be the ideal place to get an answer to this type 
question. If I am misusing the list in any way, feel free to redirect me 
to a more appropriate forum or mailing list.

Many thanks in advance for your help,


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