Hi Kay, I think the file names can be anything...so I am not sure why it didn't work for your case. If you can find a RUN_FILE_xx.log where this happens and send that to me I can try to have a look. On the other hand, if you are using a recent Rosetta v3.5 or later you do not need the fragment files any more, so that might be the best solution. Let me know if that doesn't do it! All the best, Tom T On Nov 10, 2015, at 1:07 PM, Perry, Kay H. wrote: 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 Kay Perry NE-CAT 9700 S. Cass Ave. Bldg. 436 E007 Argonne, IL 60439 630-252-0692 _______________________________________________ phenixbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]mailto:[email protected]