[modeller_usage] special restrains for aromatic packing interactions

[Thomas Evangelidis <tevang3@gmail.com>]

Dear Modellers,

I'm trying to apply restrains to the interactions of cavity residues with ATP. Apart from electrostatic interactions between atom pairs, a Tyr residue is always packed parallel with the Adenine ring of ATP, as shown in this pic:

http://personalpages.manchester.ac.uk/postgrad/Thomas.Evangelidis/aromatic_packing.png

I have labelled the atoms to help you. I'm wondering what would be the best stereochemical restrains to describe this interaction? A list with Modeller's stereochemical restrains can be found here:

http://salilab.org/modeller/manual/node196.html

Or would an Energy-based restrain describe that interactions better? Any suggestions are welcome.

thanks,
Tom