I developed a protocol with hydrogenBondConstraintGenerator integrated to enforce the hydrogen bond between N on residue 324 and O1 on residue 399 (399 is FMN, my ligand) (I plan to define more H bonds but just set 1 here to do a protocol check first). I ran 2 rounds to check whether the protocol is correct. It seems like that the atom_pair_constraint equals to 0 in the final score for both poses. But the distance between N324 and O1 399 in both poses are bigger than 2.8, which should give a positive score under atom_pair_constraint for my knowledge since I define the atom_pair_func as Harmonic 2.0 0.5… . I can not figure out what is wrong here. I attached both my xml, score and PDB file for your references.
Please suggest some possible issues.