On 2/26/10 5:32 AM, Thomas Evangelidis wrote:

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:

To model this, you'd need to add one or more additional restraints:
http://salilab.org/modeller/9v7/manual/node204.html

I'm not sure what the best form would be for a pi-stacking interaction. For stacking of two 6-membered rings, with Modeller restraints you could add 6 distance restraints between the pairs of atoms (but that would prevent rotation, of course) or create two centers of gravity, one for each ring, and add a single distance restraint between the two (but that would not force the rings to lie in the same plane - you'd have to add a few dihedral restraints to do that). If you can't achieve it with Modeller restraints, you can certainly write your own.

       Ben Webb, Modeller Caretaker
--
modeller-care@salilab.org             http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage