I am trying to run rosetta for a heterodimer with two different chains.  I have the following commands, but in some subprocesses, I get the error message: Sorry: Sorry, need 2 fragment files (3 and 9 residues) for rosetta_rebuild

I have the following in my script:

fragment_files_chain_list=V \
fragment_files_chain_list=A \
fragment_files_3_mer_by_chain="orfx3_03_05.200_v1_3" \
fragment_files_9_mer_by_chain="orfx3_09_05.200_v1_3" \
fragment_files_3_mer_by_chain="orfx1_03_05.200_v1_3" \
fragment_files_9_mer_by_chain="orfx1_09_05.200_v1_3" \

Do I need to have the chain ID in the filename?

Kay