[phenixbb] mr_rosetta problems

Ian Slaymaker slaymake at usc.edu
Tue Aug 7 09:21:21 PDT 2012

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
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

Starting job 1...Log will be:

******************* ERROR ENDING ***************
mr_rosetta failed...

Sorry, a subprocess has failed...


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:
Log for rebuilding:

**************ERROR ENDING**********************
Failed to run REBUILD...see log file in

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
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