When I run the docking script, it starts out ok, but, as the run progresses, the ligands are being placed further and further from the target substrate. Also, I get the message "protocols.docking.DockingInitialPerturbation: moving together failed. Aborting DockingSlideIntoContact."
Is there any way to constrain where the movers will place the ligands? I'm using the following command line options:
docking.py --pdb_filename hard_to_dock.pdb --partners AB_C --jobs 1000 --job_output docked --translation 3 --rotation 8 --PyMOL_Mover_ip off
Any suggestions or ideas for debugging this much appreciated.