If you mean restraints on base stacking, no, we don't have anything like this right now.  The only implementation of this anywhere, as far as I know, is the one from your (Noller) lab, but (aside from the lack of an explicit license) the fact that it's derived from CNS makes me very reluctant to even look at the code.  However, if anyone has the derivation for the restraint energy function, we'd be happy to consider adding this to Phenix - we need to make a lot of changes to how we handle base-pairing anyway.

-Nat