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    My guess is that one of the files listed in ./list-of-pdbs.txt doesn’t contain any usable atom coordinates. Check if you have any non-pdb files listed, or any empty files, or even if you have a valid PDB file, but with all zero values in the occupancy field. (By default, Rosetta discards any atoms which are listed with zero occupancy values. A quick test is to add the flag -run:trust_missing_coords to the command line, which will cause Rosetta to trust the coordinates given for zero occupancy atoms.)