[phenixbb] mr_rosetta fragment_files by chain

Terwilliger, Thomas Charles terwilliger at lanl.gov
Tue Nov 10 12:21:39 PST 2015

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 Perry
9700 S. Cass Ave.
Bldg. 436 E007
Argonne, IL 60439
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