can anyone help me correct this script to do alanine scanning

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- August 27, 2019 at 12:23 am #3235
  Anonymous
  HI,
  
  I want to do alanine scanning. I just started learning to use Rosetta. I really do not know how to fix this rosettascripts. I am wondering anyone coul please help me out. I would much appreciated.
  
  Thank you very much.
  
  /home/jinyan/rosetta3.10/rosetta_bin_linux_2018.33.60351_bundle/main/source/bin/rosetta_scripts.default.linuxgccrelease -s dreria_com_2.pdb -parser:protocol ala_scan1.xml
  
  core.init: Checking for fconfig files in pwd and ./rosetta/flags
  
  core.init: Rosetta version: rosetta.binary.linux.release-188 r188 2018.33+release.7111c54 7111c54c14ba9a53c012a524f8f1438a8e3fb020 https://www.rosettacommons.org 2018-08-14T02:36:37.119534
  
  core.init: command: /home/jinyan/rosetta3.10/rosetta_bin_linux_2018.33.60351_bundle/main/source/bin/rosetta_scripts.default.linuxgccrelease -s dreria_com_2.pdb -parser:protocol ala_scan1.xml
  
  core.init: ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=701501949 seed_offset=0 real_seed=701501949
  
  core.init.random: RandomGenerator:init: Normal mode, seed=701501949 RG_type=mt19937
  
  core.init: Resolved executable path: /home/jinyan/rosetta3.10/rosetta_bin_linux_2018.33.60351_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/rosetta_scripts.default.linuxgccrelease
  
  core.init: Looking for database based on location of executable: /home/jinyan/rosetta3.10/rosetta_bin_linux_2018.33.60351_bundle/main/database/
  
  protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter
  
  protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs
  
  protocols.jd2.PDBJobInputter: pushed dreria_com_2.pdb nstruct index 1
  
  protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active …
  
  protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
  
  protocols.jd2.PDBJobInputter: filling pose from PDB dreria_com_2.pdb
  
  core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 617 residue types
  
  core.chemical.GlobalResidueTypeSet: Total time to initialize 0.66 seconds.
  
  core.import_pose.import_pose: File ‘dreria_com_2.pdb’ automatically determined to be of type PDB
  
  core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ALA:CtermProteinFull 6
  
  protocols.rosetta_scripts.RosettaScriptsParser: dock_design_filename=ala_scan1.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 ‘dreria_com_2_0001’
  
  Error: [ ERROR ]
  
  File: src/protocols/rosetta_scripts/RosettaScriptsParser.cc:1199
  
  Input rosetta scripts XML file “ala_scan1.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
  
  Error messages were:
  
  Error: attributes construct error
  
  10:    <MOVE_MAP_FACTORIES>
  
  11:    </MOVE_MAP_FACTORIES>
  
  12:    <SIMPLE_METRICS>
  
  13:    </SIMPLE_METRICS>
  
  14:    <MOVERS>
  
  15:             <MinMover name=”min” scorefxn=”socre12″ chi=”1″ bb=”1″ cartesian=”0″/ >
  
  16:             <ddG name=”ddgmover”scorefxn=”score12″jump=”1″ repack_unbound=”true” repack_bound=”true”relax_bound=”false”relax_unbound=”true”/>
  
  17:         </MOVERS>
  
  18:         <FILTERS>
  
  19:            <DdGScan name=”alascan” task_operations=”rrf” repeats=”5″ scorefxn=”score12″report_diffs=”1″write2pdb=”1″ ddG_mover=”ddgmover”/>
  
  20:
  
  Error: Couldn’t find end of Start Tag MinMover line 15
  
  10:    <MOVE_MAP_FACTORIES>
  
  11:    </MOVE_MAP_FACTORIES>
  
  12:    <SIMPLE_METRICS>
  
  13:    </SIMPLE_METRICS>
  
  14:    <MOVERS>
  
  15:             <MinMover name=”min” scorefxn=”socre12″ chi=”1″ bb=”1″ cartesian=”0″/ >
  
  16:             <ddG name=”ddgmover”scorefxn=”score12″jump=”1″ repack_unbound=”true” repack_bound=”true”relax_bound=”false”relax_unbound=”true”/>
  
  17:         </MOVERS>
  
  18:         <FILTERS>
  
  19:            <DdGScan name=”alascan” task_operations=”rrf” repeats=”5″ scorefxn=”score12″report_diffs=”1″write2pdb=”1″ ddG_mover=”ddgmover”/>
  
  20:
  
  Error: attributes construct error
  
  11:    </MOVE_MAP_FACTORIES>
  
  12:    <SIMPLE_METRICS>
  
  13:    </SIMPLE_METRICS>
  
  14:    <MOVERS>
  
  15:             <MinMover name=”min” scorefxn=”socre12″ chi=”1″ bb=”1″ cartesian=”0″/ >
  
  16:             <ddG name=”ddgmover”scorefxn=”score12″jump=”1″ repack_unbound=”true” repack_bound=”true”relax_bound=”false”relax_unbound=”true”/>
  
  17:         </MOVERS>
  
  18:         <FILTERS>
  
  19:            <DdGScan name=”alascan” task_operations=”rrf” repeats=”5″ scorefxn=”score12″report_diffs=”1″write2pdb=”1″ ddG_mover=”ddgmover”/>
  
  20:
  
  21:    </FILTERS>
  
  Error: Couldn’t find end of Start Tag ddG line 16
  
  11:    </MOVE_MAP_FACTORIES>
  
  12:    <SIMPLE_METRICS>
  
  13:    </SIMPLE_METRICS>
  
  14:    <MOVERS>
  
  15:             <MinMover name=”min” scorefxn=”socre12″ chi=”1″ bb=”1″ cartesian=”0″/ >
  
  16:             <ddG name=”ddgmover”scorefxn=”score12″jump=”1″ repack_unbound=”true” repack_bound=”true”relax_bound=”false”relax_unbound=”true”/>
  
  17:         </MOVERS>
  
  18:         <FILTERS>
  
  19:            <DdGScan name=”alascan” task_operations=”rrf” repeats=”5″ scorefxn=”score12″report_diffs=”1″write2pdb=”1″ ddG_mover=”ddgmover”/>
  
  20:
  
  21:    </FILTERS>
  
  Error: attributes construct error
  
  14:    <MOVERS>
  
  15:             <MinMover name=”min” scorefxn=”socre12″ chi=”1″ bb=”1″ cartesian=”0″/ >
  
  16:             <ddG name=”ddgmover”scorefxn=”score12″jump=”1″ repack_unbound=”true” repack_bound=”true”relax_bound=”false”relax_unbound=”true”/>
  
  17:         </MOVERS>
  
  18:         <FILTERS>
  
  19:            <DdGScan name=”alascan” task_operations=”rrf” repeats=”5″ scorefxn=”score12″report_diffs=”1″write2pdb=”1″ ddG_mover=”ddgmover”/>
  
  20:
  
  21:    </FILTERS>
  
  22:    <MOVERS>
  
  23:    </MOVERS>
  
  24:    <PROTOCOLS>
  
  Error: Couldn’t find end of Start Tag DdGScan line 19
  
  14:    <MOVERS>
  
  15:             <MinMover name=”min” scorefxn=”socre12″ chi=”1″ bb=”1″ cartesian=”0″/ >
  
  16:             <ddG name=”ddgmover”scorefxn=”score12″jump=”1″ repack_unbound=”true” repack_bound=”true”relax_bound=”false”relax_unbound=”true”/>
  
  17:         </MOVERS>
  
  18:         <FILTERS>
  
  19:            <DdGScan name=”alascan” task_operations=”rrf” repeats=”5″ scorefxn=”score12″report_diffs=”1″write2pdb=”1″ ddG_mover=”ddgmover”/>
  
  20:
  
  21:    </FILTERS>
  
  22:    <MOVERS>
  
  23:    </MOVERS>
  
  24:    <PROTOCOLS>
  
  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: dreria_com_2_0001
  
  protocols.jd2.JobDistributor: no more batches to process…
  
  protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 5 seconds
  
  Error: [ ERROR ] Exception caught by rosetta_scripts application:
  
  File: src/protocols/jd2/JobDistributor.cc:329
  
  1 jobs failed; check output for error messages
  
  Error: [ ERROR ]
- August 27, 2019 at 1:16 am #14911
  Anonymous
  The following is my rosettascript. Please help me and take a look.
  
  Thank you in advance.
  
  Best regards
  
  Jinyan
  
  <ROSETTASCRIPTS>
  
  <SCOREFXNS>
  
  <Socrefunction name=”score12″ weights=”score12″/>
  
  </SCOREFXNS>
  
  <RESIDUE_SELECTORS>
  
  </RESIDUE_SELECTORS>
  
  <TASKOPERATIONS>
  
  <ReadResfile name=”rrf” filename=”dreria67″/>
  
  </TASKOPERATIONS>
  
  <MOVE_MAP_FACTORIES>
  
  </MOVE_MAP_FACTORIES>
  
  <SIMPLE_METRICS>
  
  </SIMPLE_METRICS>
  
  <MOVERS>
  
  <MinMover name=”min” scorefxn=”socre12″ chi=”1″ bb=”1″ cartesian=”0″/>
  
  <ddG name=”ddgmover”scorefxn=”score12″jump=”1″ repack_unbound=”true” repack_bound=”true”relax_bound=”false”relax_unbound=”true”/>
  
  </MOVERS>
  
  <FILTERS>
  
  <DdGScan name=”alascan” task_operations=”rrf” repeats=”5″ scorefxn=”score12″report_diffs=”1″write2pdb=”1″ ddG_mover=”ddgmover”/>
  
  </FILTERS>
  
  <MOVERS>
  
  </MOVERS>
  
  <PROTOCOLS>
  
  <Add mover=”min”/>
  
  <Add mover=”ddgmover”/>
  
  <Add filter=”alascan”/>
  
  </PROTOCOLS>
  
  <OUTPUT />
  
  </ROSETTASCRIPTS>
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