Hi, looking for some help,
It appears that constraints do not contribute to the final score output when running the FlexPepDock ab initio protocol.
I am getting docking samples that should yield score penalties >1000 under the provided distance constraints (AtomPair FLAT_HARMONIC). However, the scorefile reports numbers consistent with the score absent of penalties (approx -550, for a protein length 300 and peptide length 5).
I provide the constraints file with the flag -constraints:cst_file