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    I assume you’re familiar with The Matrix.

    The Blue Pill: option A above, skip the centroid perturbation step. -remodel no wasn’t input quite right somehow, because it still says “remodel perturb_kic”. Can you post the options file you tried?

    The Red Pill: look at the files (rosetta_database)/chemical/atom_type_sets/fa_standard/atom_properties.txt, chemical/atom_type_sets/centroid/atom_properties.txt, and your params file. You’ll notice your params file has atom types listed in the fa_standard atom types, NOT listed in the centroid atom types. Try modifying either centroid/atom_properties to include your ligand’s atom types (copy them from the fa_standard atom types), or modifying a copy of your ligand paramter file to use only the centroid atom types (sort of limited). This can be made to work eventually but it’s going to be a fair amount of trial and error.

    (It may also be informative to compare some of the centroid and fa_standard residue types; sub in residue_type_sets for atom_type_sets).