- This topic has 3 replies, 4 voices, and was last updated 10 years ago by Anonymous.
March 27, 2013 at 9:46 am #1541Anonymous
I tried to do some loop modeling and now I have this strange problem. Loop modeling no longer works even though I’ve used it in the past.
Rosetta seems to think that there are no residues in the pose although relax works fine on the same pdb. I tried a very simple test (see below) to try to get it to work but the result is the same. The same problem occurs in both OSX and LInux. What could be the source of this problem?
With the release version I get this message:
ERROR: Start pose and native pose don’t match in length
With the debug version I get this message:
ERROR: Residue index description given on line 0 of the file named loopmodel.loops exceeds the number of residues in the Pose: pose_index_ = 15 vs pose.total_residue() 0
My test pdb is test_in.pdb (comes with Rosetta)
70 A NATAA
71 A ALLAA
72 A ALLAA
73 A ALLAA
74 A ALLAA
75 A ALLAA
76 A ALLAA
77 A ALLAA
78 A ALLAA
79 A ALLAA
80 A NATAA
LOOP 70 80 75
March 27, 2013 at 3:00 pm #8557Anonymous
You are not the only person to report an error of this type, but I’ve never been able to duplicate it locally (I tried again just now and couldn’t). The fact that relax takes the same PDB just fine is significant. Does it go away if you don’t pass -native?
November 10, 2013 at 8:43 am #9494Anonymous
I have the same problem.
Had it been finally solved?
Is it a compilation problem or an input data problem? Or just a bug?
To test it thoroughly I used only three options in the end:
Got the message:
protocols.looprelax: ==== Loop protocol: =================================================
protocols.looprelax: remodel no
protocols.looprelax: intermedrelax no
protocols.looprelax: refine no
protocols.looprelax: relax no
protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active …
ERROR: Residue index description given on line 0 of the file named loop_file exceeds the number of residues in the Pose: pose_index_ = 1 vs pose.total_residue() 0
ERROR:: Exit from: src/protocols/loops/LoopsFileIO.cc line: 159
The problem seems to be with reading the input pdb file…
November 10, 2013 at 7:39 pm #9495Anonymous
‘-loops::input_pdb’ — This is the issue. Previous versions of the loop model application used this flag for file input. The protocol has been updated, though, to use the standard Rosetta input/output options. So now you would want to use “-s” to list the input PDB instead.
Sorry that we didn’t give better error messages – it’s been fixed for future releases.
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