I see some strange behavior of enzyme design with ligand.
1) I have created a library of rotamers, set path to this library in params file (by PDB_ROTAMERS rotlib.pdb) and run enzyme design. But there is still only translation and rotation of rigid body in the active site and no using of the rotamer library. Only when I start with ligand structure with some clashes in the protein pdb file I can see optimization of of torsion angles of the ligand. Can you please explain how it works?
2) I have a problem with cst file. Even when I set the force constant to really high value (CONSTRAINT:: distanceAB: 2.4 0.3 999.0 0 1) I'm not able to keep the defined atoms (C and O) closer then 3 A.
I would be very grateful if someone could help,