While trying to use harmonic, or guassian, distance restaints in low resolution centroid only docking in the docking_protocol.linuxgccrelease I've encountered weird Scoretype: atom_pair_constraint score errors that prevent the output of docked proteins.
Using a single distance restiant taken from a crystallographic positions, AtomPair CA 132A CA 88B HARMONIC 46.0 5.0, model generation fails as the Scoretype: atom_pair_constraint score never reaches the cutoff of 1. However the distance restaint AtomPair CA 132A CA 88B HARMONIC 46.0 15.0 returns models with a CA-CA distance of ~46 angstroms, well within the first AtomPair restaint mean and SD of 46.0 and 5.0.
If it helps, my input file is:
-dock_pert 3 8
-mute core.util.prof ## dont show timing info
#-out:file:fullatom # Boolean flag to indicate full atom