If you look at the log file, there should be a line at the very end which reads “can not find a residue type that matches the residue (residue name) at position (position)” which should help debug things. If you can’t see it, that’s because stdout is buffered when redirected, and the line was left in the buffer (and not put to disk) when the program existed. Try re-running it with the output going to the screen, and you should see the line.
That might not be necessary, though, as my guess from looking at the code near the error is that the docking protocol is trying to go (temporarily) from full atom mode to centroid mode for one step of the protocol, and it’s not finding the centroid-mode params file for the new residues. molfile_to_params should be able to generate the centroid mode params file (I forget the exact flag – do a “molfile_to_params.py -h” for the help), and then include them in the flags file with the -extra_res_cen flag (works like -extra_res_fa, but for centroid parameters, rather than full atom).