loopmodel thinks there are no residues in the pose

[Anonymous]

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)

Resfile:
NATRO
USE_INPUT_SC
start
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

loops file:
LOOP 70 80 75

flags file:
-in:file:native test_in.pdb
-in:file:fullatom
-loops:input_pdb test_in.pdb
-loops:loop_file loopmodel.loops
-loops:remodel perturb_kic
-loops:refine refine_kic
-loops:relax fastrelax
-resfile loopmodel.resfile
-in:ignore_unrecognized_res
-overwrite
-out:pdb true
-out:file:fullatom
-out:path:pdb ./loopmodel_output
-out:nstruct 10

[Anonymous]

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?

[Anonymous]

Hi,
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:
-database
-loops::input_pdb
-loops::loop_file
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…
Any ideas?

[Anonymous]

‘-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.

[Author]

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