I am performing Rosetta protein-ligand docking and I added constraints both in centroid mode and high resolution mode, but the constraints are not used. I got a warning at the end of the log file saying :
protocols.jd2.JobDistributor: [ WARNING ] The following options have been set, but have not yet been used:
Could you help me wiht this issue? why aren't the constraints used? I do not get any errors, but the output does not meet the constraints.