how to do alanine scanning

[Anonymous]

Hi,

I want to do alanine scanning but I really do not know how to correct this rosettascripts. Could anyone please correct it. I would much appreciated.

Thanks in advance.

Best regards

JInyan

 

/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_scan2.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_scan2.xml

core.init: ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=-1482059301 seed_offset=0 real_seed=-1482059301

core.init.random: RandomGenerator:init: Normal mode, seed=-1482059301 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 0.68 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_scan2.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_scan2.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:     <SIMPLE_METRICS>

12:     </SIMPLE_METRICS>

13:     <MOVERS>

14:             <MinMover name=”min” scorefxn=”socre12″ chi=”1″ bb=”1″ cartesian=”0″/>

15:             <ddG name=”ddgmover”scorefxn=”score12″jump=”1″ repack_unbound=”true” repack_bound=”true”relax_bound=”false”relax_unbound=”true”/>

16:         </MOVERS>

17:         <FILTERS>

18:             <AlaScan name=”alascan” scorefxn=”score12″ jump=”1″ interface_distance_cutoff=”8.0″ partner1=”1″ partner2=”1″repeats=”4″>         

19:             <Ddg name=”ddg” confidence=”0″/>

20:

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

10:     </MOVE_MAP_FACTORIES>

11:     <SIMPLE_METRICS>

12:     </SIMPLE_METRICS>

13:     <MOVERS>

14:             <MinMover name=”min” scorefxn=”socre12″ chi=”1″ bb=”1″ cartesian=”0″/>

15:             <ddG name=”ddgmover”scorefxn=”score12″jump=”1″ repack_unbound=”true” repack_bound=”true”relax_bound=”false”relax_unbound=”true”/>

16:         </MOVERS>

17:         <FILTERS>

18:             <AlaScan name=”alascan” scorefxn=”score12″ jump=”1″ interface_distance_cutoff=”8.0″ partner1=”1″ partner2=”1″repeats=”4″>         

19:             <Ddg name=”ddg” confidence=”0″/>

20:

Error: attributes construct error

13:     <MOVERS>

14:             <MinMover name=”min” scorefxn=”socre12″ chi=”1″ bb=”1″ cartesian=”0″/>

15:             <ddG name=”ddgmover”scorefxn=”score12″jump=”1″ repack_unbound=”true” repack_bound=”true”relax_bound=”false”relax_unbound=”true”/>

16:         </MOVERS>

17:         <FILTERS>

18:             <AlaScan name=”alascan” scorefxn=”score12″ jump=”1″ interface_distance_cutoff=”8.0″ partner1=”1″ partner2=”1″repeats=”4″>  

19:             <Ddg name=”ddg” confidence=”0″/>

20:

21:     </FILTERS>

22:     <MOVERS>

23:     </MOVERS>

Error: Couldn’t find end of Start Tag AlaScan line 18

13:     <MOVERS>

14:             <MinMover name=”min” scorefxn=”socre12″ chi=”1″ bb=”1″ cartesian=”0″/>

15:             <ddG name=”ddgmover”scorefxn=”score12″jump=”1″ repack_unbound=”true” repack_bound=”true”relax_bound=”false”relax_unbound=”true”/>

16:         </MOVERS>

17:         <FILTERS>

18:             <AlaScan name=”alascan” scorefxn=”score12″ jump=”1″ interface_distance_cutoff=”8.0″ partner1=”1″ partner2=”1″repeats=”4″>         

19:             <Ddg name=”ddg” confidence=”0″/>

20:

21:     </FILTERS>

22:     <MOVERS>

23:     </MOVERS>

---

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 ]

 

 

 

 

 

 

 

[Anonymous]

The following is my script. Could you please help me correct it. 

Thank you in advance.

Best regards

Jinyan 

<ROSETTASCRIPTS>

        <SCOREFXNS>

           <Socrefunction name=”score12″ weights=”score12″/>

        </SCOREFXNS>

        <RESIDUE_SELECTORS>

        </RESIDUE_SELECTORS>

        <TASKOPERATIONS>

        </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>

            <AlaScan name=”alascan” scorefxn=”score12″ jump=”1″ interface_distance_cutoff=”8.0″ partner1=”1″ partner2=”1″repeats=”4″>

            <Ddg name=”ddg” confidence=”0″/>

        </FILTERS>

        <MOVERS>

        </MOVERS>

        <PROTOCOLS>

          <Add mover=”min”/>

         <Add mover=”ddgmover”/>

         <Add filter=”alascan”/>

         <Add filter=”ddg”/>

        </PROTOCOLS>

        <OUTPUT />

</ROSETTASCRIPTS>

 

[Anonymous]

ROSETTASCRIPTS>

<SCOREFXNS>

<Socrefunction name="score12" weights="score12"/>

</SCOREFXNS>

<RESIDUE_SELECTORS>

</RESIDUE_SELECTORS>

<TASKOPERATIONS>

</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>

<AlaScan name="alascan" scorefxn="score12" jump="1" interface_distance_cutoff="8.0" partner1="1" partner2="1" repeats="4"/>

<Ddg name="ddg" confidence="0"/>



</FILTERS>

<MOVERS>

</MOVERS>

<PROTOCOLS>

<Add mover="min"/>

<Add mover="ddgmover"/>

<Add filter="alascan"/>

<Add filter="ddg"/>



</PROTOCOLS>

<OUTPUT />

</ROSETTASCRIPTS>

you’re missing the ‘/’ at the end of AlaScan?

also in the ddG mover you’re missing a bunch of spaces between the parameter names and the values :

ie:

partner2=”1″repeats=”4″>

 

[Anonymous]

Also, at the beginning of your script, you misspelled “score” as “socre” a couple of times.

[Anonymous]

Thank you very much!!!!!!

[Anonymous]

Thank you very much!!!!!!!!

[Author]

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