Error during running a tutorial

[Anonymous]

Hello, 

I am trying to run a tutorail (rosetta-mdff-tutorial.pdf; 3.1 Structure prediction section) but I get an error during vmd -dispdev text -e fold_rpn11_terminus.tcl or more exactly during start_rosetta_abinitio rpn11_terminus rpn11_yeast_23-306_complete [list “resid 196 to 284”] 1 [list [list “rpn11_yeast_23-306_frag9” “rpn11_yeast_23-306_frag3”]] [pwd]/input $nstruct 0 0 0. Please see its log below.

I did not notice any error during compilation of Rosetta. I would be very appreciate if somebody could tell me what is wrong or what to check.

Thank you in advance!

Best regards,

Maria.

 

---

core.init: Rosetta version rosetta.source.release-156:b1dc16ff17da7a38b52c000abb74f85e4f0333c8 2017-10-27 12:03:34.443146 from http://www.rosettacommons.org

core.init: command: /gs/project/ear-065-aa/rosetta_src_2017.45.59812_bundle/main/source/bin/rosetta_scripts.linuxgccrelease -database /gs/project/ear-065-aa/rosetta_src_2017.45.59812_bundle/main/database -nstruct 100 -out::prefix rpn11_terminus_ -s ../full_length_model/rpn11_yeast_23-306_complete.pdb -parser::protocol ../rosetta_input_rpn11_terminus/rpn11_terminus.xml -parser:view -ignore_zero_occupancy false -overwrite

core.init: ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=-671816631 seed_offset=0 real_seed=-671816631

core.init.random: RandomGenerator:init: Normal mode, seed=-671816631 RG_type=mt19937

protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter

protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs

protocols.jd2.PDBJobInputter: pushed ../full_length_model/rpn11_yeast_23-306_complete.pdb nstruct indices 1 – 100

protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active … 

protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job

protocols.jd2.PDBJobInputter: filling pose from PDB ../full_length_model/rpn11_yeast_23-306_complete.pdb

core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set.  Created 569 residue types

core.chemical.GlobalResidueTypeSet: Total time to initialize 0.75 seconds.

core.import_pose.import_pose: File ‘../full_length_model/rpn11_yeast_23-306_complete.pdb’ automatically determined to be of type PDB

protocols.rosetta_scripts.RosettaScriptsParser: dock_design_filename=../rosetta_input_rpn11_terminus/rpn11_terminus.xml

protocols.rosetta_scripts.RosettaScriptsParser: Generating XML Schema for rosetta_scripts…

protocols.rosetta_scripts.RosettaScriptsParser: …done

protocols.rosetta_scripts.RosettaScriptsParser: Initializing schema validator…

protocols.rosetta_scripts.RosettaScriptsParser: …done

protocols.rosetta_scripts.RosettaScriptsParser: Validating input script…

Error: [ ERROR ] ERROR: Exception caught by JobDistributor while trying to get pose from job ‘rpn11_terminus_rpn11_yeast_23-306_complete_0001’

Error: [ ERROR ] Input rosetta scripts XML file “../rosetta_input_rpn11_terminus/rpn11_terminus.xml” failed to validate against the rosetta scripts schema. Use the option -parser::output_schema <output filename> to output the schema to a file to see all valid options.

Your XML has failed validation.  The error message below will tell you where in your XML file the error occurred.  Here’s how to fix it:

1) If the validation fails on something obvious, like an illegal attribute due to a spelling error (perhaps you used scorefnction instead of scorefunction), then you need to fix your XML file.

2) If you haven’t run the XML rewriter script and this might be pre-2017 Rosetta XML, run the rewriter script (tools/xsd_xrw/rewrite_rosetta_script.py) on your input XML first.  The attribute values not being in quotes (scorefunction=talaris2014 instead of scorefunction=”talaris2014″) is a good indicator that this is your problem.

3) If you are a developer and neither 1 nor 2 worked – email the developer’s mailing list or try Slack.

4) If you are an academic or commercial user – try the Rosetta Forums https://www.rosettacommons.org/forum

5)

Error messages were:

Error: AttValue: ” or ‘ expected

1: <ROSETTASCRIPTS>

2: <RESIDUE_SELECTORS>

3: <Index name=fix resnums=”1-173,263-284″ />

4: <Chain name=ChainA chains=”A” /> 

5: </RESIDUE_SELECTORS>

6: <MOVERS>

7: <SwitchResidueTypeSetMover name=centroid set=”centroid” /> 

8: <RigidChunkCM name=chunk region_selector=fix template=”/gs/project/ear-065-aa/tutorial/full_length_model/rpn11_yeast_23-306_complete.pdb” selector=fix apply_to_template=centroid />

Error: attributes construct error

1: <ROSETTASCRIPTS>

2: <RESIDUE_SELECTORS>

3: <Index name=fix resnums=”1-173,263-284″ />

4: <Chain name=ChainA chains=”A” /> 

5: </RESIDUE_SELECTORS>

6: <MOVERS>

7: <SwitchResidueTypeSetMover name=centroid set=”centroid” /> 

8: <RigidChunkCM name=chunk region_selector=fix template=”/gs/project/ear-065-aa/tutorial/full_length_model/rpn11_yeast_23-306_complete.pdb” selector=fix apply_to_template=centroid />

Error: Couldn’t find end of Start Tag Index line 3

1: <ROSETTASCRIPTS>

2: <RESIDUE_SELECTORS>

3: <Index name=fix resnums=”1-173,263-284″ />

4: <Chain name=ChainA chains=”A” /> 

5: </RESIDUE_SELECTORS>

6: <MOVERS>

7: <SwitchResidueTypeSetMover name=centroid set=”centroid” /> 

8: <RigidChunkCM name=chunk region_selector=fix template=”/gs/project/ear-065-aa/tutorial/full_length_model/rpn11_yeast_23-306_complete.pdb” selector=fix apply_to_template=centroid />

Error: AttValue: ” or ‘ expected

1: <ROSETTASCRIPTS>

2: <RESIDUE_SELECTORS>

3: <Index name=fix resnums=”1-173,263-284″ />

4: <Chain name=ChainA chains=”A” /> 

5: </RESIDUE_SELECTORS>

6: <MOVERS>

7: <SwitchResidueTypeSetMover name=centroid set=”centroid” /> 

8: <RigidChunkCM name=chunk region_selector=fix template=”/gs/project/ear-065-aa/tutorial/full_length_model/rpn11_yeast_23-306_complete.pdb” selector=fix apply_to_template=centroid />

9: <AbscriptMover name=abinitio cycles=2 >

Error: attributes construct error

1: <ROSETTASCRIPTS>

2: <RESIDUE_SELECTORS>

3: <Index name=fix resnums=”1-173,263-284″ />

4: <Chain name=ChainA chains=”A” /> 

5: </RESIDUE_SELECTORS>

6: <MOVERS>

7: <SwitchResidueTypeSetMover name=centroid set=”centroid” /> 

8: <RigidChunkCM name=chunk region_selector=fix template=”/gs/project/ear-065-aa/tutorial/full_length_model/rpn11_yeast_23-306_complete.pdb” selector=fix apply_to_template=centroid />

9: <AbscriptMover name=abinitio cycles=2 >

Error: Couldn’t find end of Start Tag Chain line 4

1: <ROSETTASCRIPTS>

2: <RESIDUE_SELECTORS>

3: <Index name=fix resnums=”1-173,263-284″ />

4: <Chain name=ChainA chains=”A” /> 

5: </RESIDUE_SELECTORS>

6: <MOVERS>

7: <SwitchResidueTypeSetMover name=centroid set=”centroid” /> 

8: <RigidChunkCM name=chunk region_selector=fix template=”/gs/project/ear-065-aa/tutorial/full_length_model/rpn11_yeast_23-306_complete.pdb” selector=fix apply_to_template=centroid />

9: <AbscriptMover name=abinitio cycles=2 >

Error: AttValue: ” or ‘ expected

 2: <RESIDUE_SELECTORS>

 3: <Index name=fix resnums=”1-173,263-284″ />

 4: <Chain name=ChainA chains=”A” /> 

 5: </RESIDUE_SELECTORS>

 6: <MOVERS>

 7: <SwitchResidueTypeSetMover name=centroid set=”centroid” /> 

 8: <RigidChunkCM name=chunk region_selector=fix template=”/gs/project/ear-065-aa/tutorial/full_length_model/rpn11_yeast_23-306_complete.pdb” selector=fix apply_to_template=centroid />

 9: <AbscriptMover name=abinitio cycles=2 >

10: <Fragments large_frags=”/gs/project/ear-065-aa/tutorial/input/rpn11_yeast_23-306_frag9″ small_frags=”/gs/project/ear-065-aa/tutorial/input/rpn11_yeast_23-306_frag3″ selector=ChainA /> 

11: </AbscriptMover> 

12: <SwitchResidueTypeSetMover name=fullatom set=”fa_standard” />

Error: attributes construct error

 2: <RESIDUE_SELECTORS>

 3: <Index name=fix resnums=”1-173,263-284″ />

 4: <Chain name=ChainA chains=”A” /> 

 5: </RESIDUE_SELECTORS>

 6: <MOVERS>

 7: <SwitchResidueTypeSetMover name=centroid set=”centroid” /> 

 8: <RigidChunkCM name=chunk region_selector=fix template=”/gs/project/ear-065-aa/tutorial/full_length_model/rpn11_yeast_23-306_complete.pdb” selector=fix apply_to_template=centroid />

 9: <AbscriptMover name=abinitio cycles=2 >

10: <Fragments large_frags=”/gs/project/ear-065-aa/tutorial/input/rpn11_yeast_23-306_frag9″ small_frags=”/gs/project/ear-065-aa/tutorial/input/rpn11_yeast_23-306_frag3″ selector=ChainA /> 

11: </AbscriptMover> 

12: <SwitchResidueTypeSetMover name=fullatom set=”fa_standard” />

Error: Couldn’t find end of Start Tag SwitchResidueTypeSetMover line 7

 2: <RESIDUE_SELECTORS>

 3: <Index name=fix resnums=”1-173,263-284″ />

 4: <Chain name=ChainA chains=”A” /> 

 5: </RESIDUE_SELECTORS>

 6: <MOVERS>

 7: <SwitchResidueTypeSetMover name=centroid set=”centroid” /> 

 8: <RigidChunkCM name=chunk region_selector=fix template=”/gs/project/ear-065-aa/tutorial/full_length_model/rpn11_yeast_23-306_complete.pdb” selector=fix apply_to_template=centroid />

 9: <AbscriptMover name=abinitio cycles=2 >

10: <Fragments large_frags=”/gs/project/ear-065-aa/tutorial/input/rpn11_yeast_23-306_frag9″ small_frags=”/gs/project/ear-065-aa/tutorial/input/rpn11_yeast_23-306_frag3″ selector=ChainA /> 

11: </AbscriptMover> 

12: <SwitchResidueTypeSetMover name=fullatom set=”fa_standard” />

Error: AttValue: ” or ‘ expected

 3: <Index name=fix resnums=”1-173,263-284″ />

 4: <Chain name=ChainA chains=”A” /> 

 5: </RESIDUE_SELECTORS>

 6: <MOVERS>

 7: <SwitchResidueTypeSetMover name=centroid set=”centroid” /> 

 8: <RigidChunkCM name=chunk region_selector=fix template=”/gs/project/ear-065-aa/tutorial/full_length_model/rpn11_yeast_23-306_complete.pdb” selector=fix apply_to_template=centroid />

 9: <AbscriptMover name=abinitio cycles=2 >

10: <Fragments large_frags=”/gs/project/ear-065-aa/tutorial/input/rpn11_yeast_23-306_frag9″ small_frags=”/gs/project/ear-065-aa/tutorial/input/rpn11_yeast_23-306_frag3″ selector=ChainA /> 

11: </AbscriptMover> 

12: <SwitchResidueTypeSetMover name=fullatom set=”fa_standard” />

13: <Environment name=env auto_cut=true> 

Error: attributes construct error

 3: <Index name=fix resnums=”1-173,263-284″ />

 4: <Chain name=ChainA chains=”A” /> 

 5: </RESIDUE_SELECTORS>

 6: <MOVERS>

 7: <SwitchResidueTypeSetMover name=centroid set=”centroid” /> 

 8: <RigidChunkCM name=chunk region_selector=fix template=”/gs/project/ear-065-aa/tutorial/full_length_model/rpn11_yeast_23-306_complete.pdb” selector=fix apply_to_template=centroid />

 9: <AbscriptMover name=abinitio cycles=2 >

10: <Fragments large_frags=”/gs/project/ear-065-aa/tutorial/input/rpn11_yeast_23-306_frag9″ small_frags=”/gs/project/ear-065-aa/tutorial/input/rpn11_yeast_23-306_frag3″ selector=ChainA /> 

11: </AbscriptMover> 

12: <SwitchResidueTypeSetMover name=fullatom set=”fa_standard” />

13: <Environment name=env auto_cut=true> 

Error: Couldn’t find end of Start Tag RigidChunkCM line 8

 3: <Index name=fix resnums=”1-173,263-284″ />

 4: <Chain name=ChainA chains=”A” /> 

 5: </RESIDUE_SELECTORS>

 6: <MOVERS>

 7: <SwitchResidueTypeSetMover name=centroid set=”centroid” /> 

 8: <RigidChunkCM name=chunk region_selector=fix template=”/gs/project/ear-065-aa/tutorial/full_length_model/rpn11_yeast_23-306_complete.pdb” selector=fix apply_to_template=centroid />

 9: <AbscriptMover name=abinitio cycles=2 >

10: <Fragments large_frags=”/gs/project/ear-065-aa/tutorial/input/rpn11_yeast_23-306_frag9″ small_frags=”/gs/project/ear-065-aa/tutorial/input/rpn11_yeast_23-306_frag3″ selector=ChainA /> 

11: </AbscriptMover> 

12: <SwitchResidueTypeSetMover name=fullatom set=”fa_standard” />

13: <Environment name=env auto_cut=true> 

Error: AttValue: ” or ‘ expected

 4: <Chain name=ChainA chains=”A” /> 

 5: </RESIDUE_SELECTORS>

 6: <MOVERS>

 7: <SwitchResidueTypeSetMover name=centroid set=”centroid” /> 

 8: <RigidChunkCM name=chunk region_selector=fix template=”/gs/project/ear-065-aa/tutorial/full_length_model/rpn11_yeast_23-306_complete.pdb” selector=fix apply_to_template=centroid />

 9: <AbscriptMover name=abinitio cycles=2 >

10: <Fragments large_frags=”/gs/project/ear-065-aa/tutorial/input/rpn11_yeast_23-306_frag9″ small_frags=”/gs/project/ear-065-aa/tutorial/input/rpn11_yeast_23-306_frag3″ selector=ChainA /> 

11: </AbscriptMover> 

12: <SwitchResidueTypeSetMover name=fullatom set=”fa_standard” />

13: <Environment name=env auto_cut=true> 

14: <Register mover=chunk />

Error: attributes construct error

 4: <Chain name=ChainA chains=”A” /> 

 5: </RESIDUE_SELECTORS>

 6: <MOVERS>

 7: <SwitchResidueTypeSetMover name=centroid set=”centroid” /> 

 8: <RigidChunkCM name=chunk region_selector=fix template=”/gs/project/ear-065-aa/tutorial/full_length_model/rpn11_yeast_23-306_complete.pdb” selector=fix apply_to_template=centroid />

 9: <AbscriptMover name=abinitio cycles=2 >

10: <Fragments large_frags=”/gs/project/ear-065-aa/tutorial/input/rpn11_yeast_23-306_frag9″ small_frags=”/gs/project/ear-065-aa/tutorial/input/rpn11_yeast_23-306_frag3″ selector=ChainA /> 

11: </AbscriptMover> 

12: <SwitchResidueTypeSetMover name=fullatom set=”fa_standard” />

13: <Environment name=env auto_cut=true> 

14: <Register mover=chunk />

Error: Couldn’t find end of Start Tag AbscriptMover line 9

 4: <Chain name=ChainA chains=”A” /> 

 5: </RESIDUE_SELECTORS>

 6: <MOVERS>

 7: <SwitchResidueTypeSetMover name=centroid set=”centroid” /> 

 8: <RigidChunkCM name=chunk region_selector=fix template=”/gs/project/ear-065-aa/tutorial/full_length_model/rpn11_yeast_23-306_complete.pdb” selector=fix apply_to_template=centroid />

 9: <AbscriptMover name=abinitio cycles=2 >

10: <Fragments large_frags=”/gs/project/ear-065-aa/tutorial/input/rpn11_yeast_23-306_frag9″ small_frags=”/gs/project/ear-065-aa/tutorial/input/rpn11_yeast_23-306_frag3″ selector=ChainA /> 

11: </AbscriptMover> 

12: <SwitchResidueTypeSetMover name=fullatom set=”fa_standard” />

13: <Environment name=env auto_cut=true> 

14: <Register mover=chunk />

Error: AttValue: ” or ‘ expected

 5: </RESIDUE_SELECTORS>

 6: <MOVERS>

 7: <SwitchResidueTypeSetMover name=centroid set=”centroid” /> 

 8: <RigidChunkCM name=chunk region_selector=fix template=”/gs/project/ear-065-aa/tutorial/full_length_model/rpn11_yeast_23-306_complete.pdb” selector=fix apply_to_template=centroid />

 9: <AbscriptMover name=abinitio cycles=2 >

10: <Fragments large_frags=”/gs/project/ear-065-aa/tutorial/input/rpn11_yeast_23-306_frag9″ small_frags=”/gs/project/ear-065-aa/tutorial/input/rpn11_yeast_23-306_frag3″ selector=ChainA /> 

11: </AbscriptMover> 

12: <SwitchResidueTypeSetMover name=fullatom set=”fa_standard” />

13: <Environment name=env auto_cut=true> 

14: <Register mover=chunk />

15: <Apply mover=abinitio />

Error: attributes construct error

 5: </RESIDUE_SELECTORS>

 6: <MOVERS>

 7: <SwitchResidueTypeSetMover name=centroid set=”centroid” /> 

 8: <RigidChunkCM name=chunk region_selector=fix template=”/gs/project/ear-065-aa/tutorial/full_length_model/rpn11_yeast_23-306_complete.pdb” selector=fix apply_to_template=centroid />

 9: <AbscriptMover name=abinitio cycles=2 >

10: <Fragments large_frags=”/gs/project/ear-065-aa/tutorial/input/rpn11_yeast_23-306_frag9″ small_frags=”/gs/project/ear-065-aa/tutorial/input/rpn11_yeast_23-306_frag3″ selector=ChainA /> 

11: </AbscriptMover> 

12: <SwitchResidueTypeSetMover name=fullatom set=”fa_standard” />

13: <Environment name=env auto_cut=true> 

14: <Register mover=chunk />

15: <Apply mover=abinitio />

Error: Couldn’t find end of Start Tag Fragments line 10

 5: </RESIDUE_SELECTORS>

 6: <MOVERS>

 7: <SwitchResidueTypeSetMover name=centroid set=”centroid” /> 

 8: <RigidChunkCM name=chunk region_selector=fix template=”/gs/project/ear-065-aa/tutorial/full_length_model/rpn11_yeast_23-306_complete.pdb” selector=fix apply_to_template=centroid />

 9: <AbscriptMover name=abinitio cycles=2 >

10: <Fragments large_frags=”/gs/project/ear-065-aa/tutorial/input/rpn11_yeast_23-306_frag9″ small_frags=”/gs/project/ear-065-aa/tutorial/input/rpn11_yeast_23-306_frag3″ selector=ChainA /> 

11: </AbscriptMover> 

12: <SwitchResidueTypeSetMover name=fullatom set=”fa_standard” />

13: <Environment name=env auto_cut=true> 

14: <Register mover=chunk />

15: <Apply mover=abinitio />

Error: Opening and ending tag mismatch: MOVERS line 6 and AbscriptMover

 6: <MOVERS>

 7: <SwitchResidueTypeSetMover name=centroid set=”centroid” /> 

 8: <RigidChunkCM name=chunk region_selector=fix template=”/gs/project/ear-065-aa/tutorial/full_length_model/rpn11_yeast_23-306_complete.pdb” selector=fix apply_to_template=centroid />

 9: <AbscriptMover name=abinitio cycles=2 >

10: <Fragments large_frags=”/gs/project/ear-065-aa/tutorial/input/rpn11_yeast_23-306_frag9″ small_frags=”/gs/project/ear-065-aa/tutorial/input/rpn11_yeast_23-306_frag3″ selector=ChainA /> 

11: </AbscriptMover> 

12: <SwitchResidueTypeSetMover name=fullatom set=”fa_standard” />

13: <Environment name=env auto_cut=true> 

14: <Register mover=chunk />

15: <Apply mover=abinitio />

16: </Environment>

Error: AttValue: ” or ‘ expected

 7: <SwitchResidueTypeSetMover name=centroid set=”centroid” /> 

 8: <RigidChunkCM name=chunk region_selector=fix template=”/gs/project/ear-065-aa/tutorial/full_length_model/rpn11_yeast_23-306_complete.pdb” selector=fix apply_to_template=centroid />

 9: <AbscriptMover name=abinitio cycles=2 >

10: <Fragments large_frags=”/gs/project/ear-065-aa/tutorial/input/rpn11_yeast_23-306_frag9″ small_frags=”/gs/project/ear-065-aa/tutorial/input/rpn11_yeast_23-306_frag3″ selector=ChainA /> 

11: </AbscriptMover> 

12: <SwitchResidueTypeSetMover name=fullatom set=”fa_standard” />

13: <Environment name=env auto_cut=true> 

14: <Register mover=chunk />

15: <Apply mover=abinitio />

16: </Environment>

17: <FastRelax name=relax repeats=1>

Error: attributes construct error

 7: <SwitchResidueTypeSetMover name=centroid set=”centroid” /> 

 8: <RigidChunkCM name=chunk region_selector=fix template=”/gs/project/ear-065-aa/tutorial/full_length_model/rpn11_yeast_23-306_complete.pdb” selector=fix apply_to_template=centroid />

 9: <AbscriptMover name=abinitio cycles=2 >

10: <Fragments large_frags=”/gs/project/ear-065-aa/tutorial/input/rpn11_yeast_23-306_frag9″ small_frags=”/gs/project/ear-065-aa/tutorial/input/rpn11_yeast_23-306_frag3″ selector=ChainA /> 

11: </AbscriptMover> 

12: <SwitchResidueTypeSetMover name=fullatom set=”fa_standard” />

13: <Environment name=env auto_cut=true> 

14: <Register mover=chunk />

15: <Apply mover=abinitio />

16: </Environment>

17: <FastRelax name=relax repeats=1>

Error: Couldn’t find end of Start Tag SwitchResidueTypeSetMover line 12

 7: <SwitchResidueTypeSetMover name=centroid set=”centroid” /> 

 8: <RigidChunkCM name=chunk region_selector=fix template=”/gs/project/ear-065-aa/tutorial/full_length_model/rpn11_yeast_23-306_complete.pdb” selector=fix apply_to_template=centroid />

 9: <AbscriptMover name=abinitio cycles=2 >

10: <Fragments large_frags=”/gs/project/ear-065-aa/tutorial/input/rpn11_yeast_23-306_frag9″ small_frags=”/gs/project/ear-065-aa/tutorial/input/rpn11_yeast_23-306_frag3″ selector=ChainA /> 

11: </AbscriptMover> 

12: <SwitchResidueTypeSetMover name=fullatom set=”fa_standard” />

13: <Environment name=env auto_cut=true> 

14: <Register mover=chunk />

15: <Apply mover=abinitio />

16: </Environment>

17: <FastRelax name=relax repeats=1>

Error: AttValue: ” or ‘ expected

 8: <RigidChunkCM name=chunk region_selector=fix template=”/gs/project/ear-065-aa/tutorial/full_length_model/rpn11_yeast_23-306_complete.pdb” selector=fix apply_to_template=centroid />

 9: <AbscriptMover name=abinitio cycles=2 >

10: <Fragments large_frags=”/gs/project/ear-065-aa/tutorial/input/rpn11_yeast_23-306_frag9″ small_frags=”/gs/project/ear-065-aa/tutorial/input/rpn11_yeast_23-306_frag3″ selector=ChainA /> 

11: </AbscriptMover> 

12: <SwitchResidueTypeSetMover name=fullatom set=”fa_standard” />

13: <Environment name=env auto_cut=true> 

14: <Register mover=chunk />

15: <Apply mover=abinitio />

16: </Environment>

17: <FastRelax name=relax repeats=1>

18: <MoveMap> 

Error: attributes construct error

 8: <RigidChunkCM name=chunk region_selector=fix template=”/gs/project/ear-065-aa/tutorial/full_length_model/rpn11_yeast_23-306_complete.pdb” selector=fix apply_to_template=centroid />

 9: <AbscriptMover name=abinitio cycles=2 >

10: <Fragments large_frags=”/gs/project/ear-065-aa/tutorial/input/rpn11_yeast_23-306_frag9″ small_frags=”/gs/project/ear-065-aa/tutorial/input/rpn11_yeast_23-306_frag3″ selector=ChainA /> 

11: </AbscriptMover> 

12: <SwitchResidueTypeSetMover name=fullatom set=”fa_standard” />

13: <Environment name=env auto_cut=true> 

14: <Register mover=chunk />

15: <Apply mover=abinitio />

16: </Environment>

17: <FastRelax name=relax repeats=1>

18: <MoveMap> 

Error: Couldn’t find end of Start Tag Environment line 13

 8: <RigidChunkCM name=chunk region_selector=fix template=”/gs/project/ear-065-aa/tutorial/full_length_model/rpn11_yeast_23-306_complete.pdb” selector=fix apply_to_template=centroid />

 9: <AbscriptMover name=abinitio cycles=2 >

10: <Fragments large_frags=”/gs/project/ear-065-aa/tutorial/input/rpn11_yeast_23-306_frag9″ small_frags=”/gs/project/ear-065-aa/tutorial/input/rpn11_yeast_23-306_frag3″ selector=ChainA /> 

11: </AbscriptMover> 

12: <SwitchResidueTypeSetMover name=fullatom set=”fa_standard” />

13: <Environment name=env auto_cut=true> 

14: <Register mover=chunk />

15: <Apply mover=abinitio />

16: </Environment>

17: <FastRelax name=relax repeats=1>

18: <MoveMap> 

Error: AttValue: ” or ‘ expected

 9: <AbscriptMover name=abinitio cycles=2 >

10: <Fragments large_frags=”/gs/project/ear-065-aa/tutorial/input/rpn11_yeast_23-306_frag9″ small_frags=”/gs/project/ear-065-aa/tutorial/input/rpn11_yeast_23-306_frag3″ selector=ChainA /> 

11: </AbscriptMover> 

12: <SwitchResidueTypeSetMover name=fullatom set=”fa_standard” />

13: <Environment name=env auto_cut=true> 

14: <Register mover=chunk />

15: <Apply mover=abinitio />

16: </Environment>

17: <FastRelax name=relax repeats=1>

18: <MoveMap> 

19: <Chain number=1 chi=0 bb=0 /> 

Error: attributes construct error

 9: <AbscriptMover name=abinitio cycles=2 >

10: <Fragments large_frags=”/gs/project/ear-065-aa/tutorial/input/rpn11_yeast_23-306_frag9″ small_frags=”/gs/project/ear-065-aa/tutorial/input/rpn11_yeast_23-306_frag3″ selector=ChainA /> 

11: </AbscriptMover> 

12: <SwitchResidueTypeSetMover name=fullatom set=”fa_standard” />

13: <Environment name=env auto_cut=true> 

14: <Register mover=chunk />

15: <Apply mover=abinitio />

16: </Environment>

17: <FastRelax name=relax repeats=1>

18: <MoveMap> 

19: <Chain number=1 chi=0 bb=0 /> 

Error: Couldn’t find end of Start Tag Register line 14

 9: <AbscriptMover name=abinitio cycles=2 >

10: <Fragments large_frags=”/gs/project/ear-065-aa/tutorial/input/rpn11_yeast_23-306_frag9″ small_frags=”/gs/project/ear-065-aa/tutorial/input/rpn11_yeast_23-306_frag3″ selector=ChainA /> 

11: </AbscriptMover> 

12: <SwitchResidueTypeSetMover name=fullatom set=”fa_standard” />

13: <Environment name=env auto_cut=true> 

14: <Register mover=chunk />

15: <Apply mover=abinitio />

16: </Environment>

17: <FastRelax name=relax repeats=1>

18: <MoveMap> 

19: <Chain number=1 chi=0 bb=0 /> 

Error: AttValue: ” or ‘ expected

10: <Fragments large_frags=”/gs/project/ear-065-aa/tutorial/input/rpn11_yeast_23-306_frag9″ small_frags=”/gs/project/ear-065-aa/tutorial/input/rpn11_yeast_23-306_frag3″ selector=ChainA /> 

11: </AbscriptMover> 

12: <SwitchResidueTypeSetMover name=fullatom set=”fa_standard” />

13: <Environment name=env auto_cut=true> 

14: <Register mover=chunk />

15: <Apply mover=abinitio />

16: </Environment>

17: <FastRelax name=relax repeats=1>

18: <MoveMap> 

19: <Chain number=1 chi=0 bb=0 /> 

20: <Span begin=174 end=262 chi=1 bb=1 /> 

Error: attributes construct error

10: <Fragments large_frags=”/gs/project/ear-065-aa/tutorial/input/rpn11_yeast_23-306_frag9″ small_frags=”/gs/project/ear-065-aa/tutorial/input/rpn11_yeast_23-306_frag3″ selector=ChainA /> 

11: </AbscriptMover> 

12: <SwitchResidueTypeSetMover name=fullatom set=”fa_standard” />

13: <Environment name=env auto_cut=true> 

14: <Register mover=chunk />

15: <Apply mover=abinitio />

16: </Environment>

17: <FastRelax name=relax repeats=1>

18: <MoveMap> 

19: <Chain number=1 chi=0 bb=0 /> 

20: <Span begin=174 end=262 chi=1 bb=1 /> 

Error: Couldn’t find end of Start Tag Apply line 15

10: <Fragments large_frags=”/gs/project/ear-065-aa/tutorial/input/rpn11_yeast_23-306_frag9″ small_frags=”/gs/project/ear-065-aa/tutorial/input/rpn11_yeast_23-306_frag3″ selector=ChainA /> 

11: </AbscriptMover> 

12: <SwitchResidueTypeSetMover name=fullatom set=”fa_standard” />

13: <Environment name=env auto_cut=true> 

14: <Register mover=chunk />

15: <Apply mover=abinitio />

16: </Environment>

17: <FastRelax name=relax repeats=1>

18: <MoveMap> 

19: <Chain number=1 chi=0 bb=0 /> 

20: <Span begin=174 end=262 chi=1 bb=1 /> 

Error: Opening and ending tag mismatch: ROSETTASCRIPTS line 1 and Environment

11: </AbscriptMover> 

12: <SwitchResidueTypeSetMover name=fullatom set=”fa_standard” />

13: <Environment name=env auto_cut=true> 

14: <Register mover=chunk />

15: <Apply mover=abinitio />

16: </Environment>

17: <FastRelax name=relax repeats=1>

18: <MoveMap> 

19: <Chain number=1 chi=0 bb=0 /> 

20: <Span begin=174 end=262 chi=1 bb=1 /> 

21: </MoveMap> 

Error: Extra content at the end of the document

12: <SwitchResidueTypeSetMover name=fullatom set=”fa_standard” />

13: <Environment name=env auto_cut=true> 

14: <Register mover=chunk />

15: <Apply mover=abinitio />

16: </Environment>

17: <FastRelax name=relax repeats=1>

18: <MoveMap> 

19: <Chain number=1 chi=0 bb=0 /> 

20: <Span begin=174 end=262 chi=1 bb=1 /> 

21: </MoveMap> 

22: </FastRelax>

---

Warning messages were:

---

Error: [ ERROR ] 

Error: [ ERROR ] Treating failure as bad input; canceling similar jobs

protocols.jd2.FileSystemJobDistributor: job failed, reporting bad input; other jobs of same input will be canceled: rpn11_terminus_rpn11_yeast_23-306_complete_0001

protocols.jd2.JobDistributor: no more batches to process… 

protocols.jd2.JobDistributor: 100 jobs considered, 1 jobs attempted in 19 seconds

Error: [ ERROR ] Exception caught by rosetta_scripts application:1 jobs failed; check output for error messages

Error: [ ERROR ] 

 

 

 

[Anonymous]

For any case, it is my rpn11_terminus.xml

 

---

<ROSETTASCRIPTS>

<RESIDUE_SELECTORS>

<Index name=fix resnums=”1-173,263-284″ />

<Chain name=ChainA chains=”A” /> 

</RESIDUE_SELECTORS>

<MOVERS>

<SwitchResidueTypeSetMover name=centroid set=”centroid” /> 

<RigidChunkCM name=chunk region_selector=fix template=”/gs/project/ear-065-aa/tutorial/full_length_model/rpn11_yeast_23-306_complete.pdb” selector=fix apply_to_template=centroid />

<AbscriptMover name=abinitio cycles=2 >

<Fragments large_frags=”/gs/project/ear-065-aa/tutorial/input/rpn11_yeast_23-306_frag9″ small_frags=”/gs/project/ear-065-aa/tutorial/input/rpn11_yeast_23-306_frag3″ selector=ChainA /> 

</AbscriptMover> 

<SwitchResidueTypeSetMover name=fullatom set=”fa_standard” />

<Environment name=env auto_cut=true> 

<Register mover=chunk />

<Apply mover=abinitio />

</Environment>

<FastRelax name=relax repeats=1>

<MoveMap> 

<Chain number=1 chi=0 bb=0 /> 

<Span begin=174 end=262 chi=1 bb=1 /> 

</MoveMap> 

</FastRelax>

</MOVERS>

<PROTOCOLS> 

<Add mover=centroid/> 

<Add mover=env/> 

<Add mover=fullatom/> 

<Add mover=relax/> 

</PROTOCOLS> 

</ROSETTASCRIPTS>

 

[Anonymous]

About a year ago we changed the format of the RosettaScripts file to more closely match the official XML format. The error messages you see are the result of using an older XML format with a newer version of Rosetta.

Not to worry – we’ve provided a script to convert between the two formats. You just need to run something like `Rosetta/tools/xsd_xrw/rewrite_rosetta_script.py –input rpn11_terminus.xml –output rpn11_terminus_new.xml`. Then replace all mentions of the old script in the commandline and options files to  the generated ‘new’ script.  (If you have a backup of the script, specifying the same name for –input and –output should work without any further modifications needed.)

[Anonymous]

Hello, rmoretti,

Thank you for your reply! I did read about the change in the XML format but did not realize that it somehow affects the tutorial running since the xml file is created automatically.

Still I do not understand how to progress the tutorial as only thing I submit is start_rosetta_abinitio rpn11_terminus rpn11_yeast_23-306_complete [list “resid 196 to 284”] 1 [list [list “rpn11_yeast_23-306_frag9” “rpn11_yeast_23-306_frag3”]] [pwd]/input $nstruct 0 0 0 within the command vmd -dispdev text -e fold_rpn11_terminus.tcl

I suppose then that versions of rosetta, rosetta tutorial and ModelMaker scripts are mixed up somehow.

Now I use rosetta_src_2017.45.59812_bundle and rosetta-mdff-tutorial.pdf from http://www.ks.uiuc.edu/Training/Tutorials/science/rosetta-mdff/rosetta-mdff-tutorial.pdf, which seem to work well together, and ModelMaker files from http://www.ks.uiuc.edu/Training/Tutorials/science/rosetta-mdff/rosetta-mdff-tutorial-files/ModelMaker/, which create the XML file in the old XML format (if you are right about the issue).

Where could I find updated ModelMaker scripts or what is the best way to modify them?

I also tried to use the ModelMaker scripts from https://github.com/ryanmcgreevy/ModelMaker, but they differ a lot. I could not see an obvious way how to use them for the tutorial (and I am not sure that this version creates the XML file in new XML format since I tried to replace a block “ROSETTA XML SCRIPT” in proc ::RosettaInputGenerator::rosetta_abinitio and got the same error).

Best regards,

Maria.

 

 

 

 

[Anonymous]

Oh, I have added 2 strings in rosetta_inpur_generator.tcl. It seems like a way around but it works.

exec mv rosetta_input_$jobname/$jobname.xml rosetta_input_$jobname/oldformat_$jobname.xml

exec /gs/project/ear-065-aa/rosetta_src_2017.45.59812_bundle/tools/xsd_xrw/rewrite_rosetta_script.py –input rosetta_input_$jobname/oldformat_$jobname.xml  –output rosetta_input_$jobname/$jobname.xml

Still trying to pass through without errors although.

Best regards,

Maria.

[Anonymous]

Hmm … as ModelMaker is an external tool that uses Rosetta (rather than part of Rosetta itself), I don’t have much experience or control of how ModelMaker is generating the XML. I would highly encourage you to get in contact with the ModelMaker author (e.g. through the GitHub “Issues” page), to see if they have a version which is compatible with the new RosettaScripts XML syntax. (It should be a rather simple fix on their part — mostly it’s adding quotation marks around options.)

Failing that, you can always try running ModelMaker with a previous version of Rosetta. You should be able to download and install an older version of Rosetta (such as Rosetta 3.7) alongside the recent Rosetta you have. Then you can point your version of ModelMaker to the older version of Rosetta, which should be compatible with the RosettaScripts XMLs that ModelMaker is generating.

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