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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Hi Ian,
<div>I think that this part of the error message is the best hint:</div>
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<div id="divRpF534913" style="direction: ltr; "><font face="Tahoma" size="2" color="#000000"><b>From:</b> phenixbb-bounces@phenix-online.org [phenixbb-bounces@phenix-online.org] on behalf of Ian Slaymaker [slaymake@usc.edu]<br>
<b>Sent:</b> Tuesday, August 07, 2012 10:21 AM<br>
<b>To:</b> phenixbb@phenix-online.org<br>
<b>Subject:</b> [phenixbb] mr_rosetta problems<br>
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<div><span style="font-family:arial,helvetica,sans-serif">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 </span><span style="font-family:arial,helvetica,sans-serif">phenix_regression.wizards.test_command_line_rosetta_quick_tests
tests went smoothly were completed. </span></div>
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<div><span style="font-family:arial,helvetica,sans-serif">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 </span><span style="font-family:arial,helvetica,sans-serif">but I am not sure exactly what they are supposed to look like</span><span style="font-family:arial,helvetica,sans-serif">.</span></div>
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<div>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? </div>
<div>The aligned model looks somewhat what I expected it to (same beta sheet arrangement) but it seems to be incomplete.</div>
<div>Any help would be very much appreciated!</div>
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<pre><font face="arial, helvetica, sans-serif">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
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<pre><font face="arial, helvetica, sans-serif">The rebuild log had repeats of several errors that I am not sure how to address:</font></pre>
<pre><font face="tahoma, sans-serif">core.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue PHE 3 (repeated several times)</font></pre>
<pre><font face="tahoma, sans-serif">core.fragments.ConstantLengthFragSet: line too short: Skipping line ' (repeated several times)</font></pre>
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<div><font face="tahoma, sans-serif">core.fragments.ConstantLengthFragSet: finished reading top 0 0mer fragments from file/dataFiles/aat000_03_05.200_v1_3</font></div>
<div><font face="tahoma, sans-serif">protocols.loops.loops_main: Frag libraries debug none 1</font></div>
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