Thanks for the suggestions! I’m now running into a different problem. When I run the docking with constraints, I see two error messages that say “protocols.docking.DockingProtocol: Danger Will Robinson! Constraints not supported in docking. Do not use. You will be sad.”
If I’m running both low- and high-resolution docking, the docking run continues on, but constraints are clearly not affecting the results or the scoring. If I’m running with the -low_res_protocol_only flag on, then the docking run quits immediately after these errors with a Segmentation Fault. Any ideas as to what might be causing this?