I am having the same problem. The line refrred to in the error talks about the occupancy entries in the pdb file, but it doesn’t help when I set them all to 1.00.
command: /home/rosetta-3.2/rosetta_source/bin/FlexPepDocking.linuxgccrelease -s input.pdb -database /home/rosetta-3.2/rosetta_database/ -flexpep_prepack -ex1 -ex2aro
An idea of what the problem is would be appreciated.
EDIT: OK it works so long as the native structure is included in the command