I am attempting to run a blind dock of a ligand (chain X) into a protein complex (chains ABCDEF). However, try as I might, I seem to always encounter problems. Currently, despite the fact that the flags I'm using should perturb the ligand by a significant amount, the resulting structures are virtually identical (for all chains) to the starting structure, except all chains have been rotated.
Here are my current command line flags:
-docking:uniform_trans 20 # angstroms
-out:mute protocols.geometry.RB_geometry core.scoring.dunbrack.SingleLigandRotamerLibrary core.scoring.rms_util
I've added and removed a number of these trying to get a different result and so far have not been successful. I'd really appreciate any insight anyone can offer on this!