I am doing enzyme design using a cst file and it seems that my constraint file is not properly defined.
I wish to define constraints such that the peptide N forms hydrogen bond with my ligand in the binding pocket. At the same time I would like this residue to be any other residue except proline. So i defined my cst as follows;
TEMPLATE:: ATOM_MAP: 1 atom_name: O8 P1 O7
TEMPLATE:: ATOM_MAP: 1 residue3: EY1
TEMPLATE:: ATOM_MAP: 2 atom_type: Nbb
TEMPLATE:: ATOM_MAP: 2 residue1: ACDEFGHIKLMNQRSTVWY
CONSTRAINT:: distanceAB: 3.20 0.20 50.00 0
CONSTRAINT:: angle_A: 153.00 20.00 50.00 360.00
CONSTRAINT:: angle_B: 110.00 20.00 50.00 360.00
CONSTRAINT:: torsion_A: -60.40 20.00 50.00 360.00
I also used a resfile which did not affect the residues in the cst file. However, I noticed that this constraint is not respected as the native residue found in the starting pdb is maintained in all designed structures. Is this the correct way to define a hbond constraint formed by any residue?
Thanks in advance for your expert help.