I am trying to get mr_rosetta working on our cluster and am running into some problems I am not sure how to solve. The phenix_regression.wizards.test_command_line_rosetta_quick_tests tests went smoothly were completed. However, my first test run with all the defaults (not submitted to multiple processors) using my reflection file, HHR analysis file, sequence file, and the 2 fragment files failed with the below errors. I checked all the files, and it seems this is a problem with the fragment files but I am not sure exactly what they are supposed to look like. I thought it could be because our cluster doesnt have access to any outside networks...is this a problem with rosetta not being able to download pdb files? if so, is there a way to supply them internally? The aligned model looks somewhat what I expected it to (same beta sheet arrangement) but it seems to be incomplete. Any help would be very much appreciated! Splitting work into 100 jobs and running with 1 processors using sh background=None in /MR_ROSETTA_1/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1 Starting job 1...Log will be: /MR_ROSETTA_1/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_FILE_1.log ******************* ERROR ENDING *************** mr_rosetta failed... ******************************************************************************** Sorry, a subprocess has failed... END OF LOG FILE /MR_ROSETTA_1/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_FILE_1.log : to match the actual PDB sequence: (protein sequence) New alignment line 4 for PDB: (protein sequence) Start position of target sequence in sequence file: 0 Aligned model for comparison: /MR_ROSETTA_1/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_1/WORK_1/aligned_model.pdb Log for rebuilding: /MR_ROSETTA_1/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_1/WORK_1/rebuild.log **************ERROR ENDING********************** Failed to run REBUILD...see log file in /MR_ROSETTA_1/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_1/WORK_1/rebuild.log The rebuild log had repeats of several errors that I am not sure how to address: core.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue PHE 3 (repeated several times) core.fragments.ConstantLengthFragSet: line too short: Skipping line ' (repeated several times) core.fragments.ConstantLengthFragSet: finished reading top 0 0mer fragments from file/dataFiles/aat000_03_05.200_v1_3 protocols.loops.loops_main: Frag libraries debug none 1