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XML schema file taken from Rosie docking giving errors in Rosetta Scripts

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XML schema file taken from Rosie docking giving errors in Rosetta Scripts
#1

Hello!

I am doing a ligand docking study and was previously using an edited XML file that I found online for performing ligand docking. I wasn't getting the same quality of results using Rosetta Scripts with the xml file that I found online, as I was with Rosie Ligand docking. To make the parameters the same I downloaded the Rosie ligand docking xml file and am attempting to use it for my Rosetta Scripts program. The problem is when I do this i get the following errors. I persume there is something wrong with my layout however this is the exact xml file that Rosie ligand docking used so I am confused as to what I have to change to get Rosetta Scripts to succesfully process it. Thank you so much.

I attached the dock.xml file as a txt file

 

[ ERROR ]: Caught exception:

File: src/protocols/rosetta_scripts/RosettaScriptsParser.cc:1207

Input rosetta scripts XML file "dock.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:

From line 4:

Error: Element 'ligand_soft_rep': This element is not expected. Expected is ( ScoreFunction ).

 

1: <ROSETTASCRIPTS>

2: 

3: <SCOREFXNS>

4: <ligand_soft_rep weights="ligand_soft_rep">

5:     <Reweight scoretype="fa_elec" weight="0.42"/>

6:     <Reweight scoretype="hbond_bb_sc" weight="1.3"/>

7:     <Reweight scoretype="hbond_sc" weight="1.3"/>

8:     <Reweight scoretype="rama" weight="0.2"/>

9: </ligand_soft_rep>

From line 20:

Error: Element 'docking_sidechain': This element is not expected. Expected is ( LigandArea ).

 

15:     <Reweight scoretype="hbond_sc" weight="1.3"/>

16:     <Reweight scoretype="rama" weight="0.2"/>

17: </hard_rep>

18:      </SCOREFXNS>

19:      <LIGAND_AREAS>

20: <docking_sidechain chain="X" cutoff="6.0" add_nbr_radius="true" all_atom_mode="true" minimize_ligand="10"/>

21: <final_sidechain chain="X" cutoff="6.0" add_nbr_radius="true" all_atom_mode="true"/>

22: <final_backbone chain="X" cutoff="7.0" add_nbr_radius="false" all_atom_mode="true" Calpha_restraints="0.3"/>

23: </LIGAND_AREAS>

24: 

25: <INTERFACE_BUILDERS>

From line 26:

Error: Element 'side_chain_for_docking': This element is not expected. Expected is ( InterfaceBuilder ).

 

21: <final_sidechain chain="X" cutoff="6.0" add_nbr_radius="true" all_atom_mode="true"/>

22: <final_backbone chain="X" cutoff="7.0" add_nbr_radius="false" all_atom_mode="true" Calpha_restraints="0.3"/>

23: </LIGAND_AREAS>

24: 

25: <INTERFACE_BUILDERS>

26: <side_chain_for_docking ligand_areas="docking_sidechain"/>

27: <side_chain_for_final ligand_areas="final_sidechain"/>

28: <backbone ligand_areas="final_backbone" extension_window="3"/>

29: </INTERFACE_BUILDERS>

30: 

31: <MOVEMAP_BUILDERS>

From line 32:

Error: Element 'docking': This element is not expected. Expected is ( MoveMapBuilder ).

 

27: <side_chain_for_final ligand_areas="final_sidechain"/>

28: <backbone ligand_areas="final_backbone" extension_window="3"/>

29: </INTERFACE_BUILDERS>

30: 

31: <MOVEMAP_BUILDERS>

32: <docking sc_interface="side_chain_for_docking" minimize_water="true"/>

33: <final sc_interface="side_chain_for_final" bb_interface="backbone" minimize_water="true"/>

34: </MOVEMAP_BUILDERS>

35: 

36: <SCORINGGRIDS ligand_chain="X" width="30.0">

37: <vdw grid_type="ClassicGrid" weight="1.0"/>

From line 37:

Error: Element 'vdw': This element is not expected. Expected is one of ( AtrGrid, ChargeGrid, ClassicGrid, HbaGrid, HbdGrid, LigandPropertyScore, PCSMultiGrid, PCSSingleGrid, RepGrid, ShapeGrid ).

 

32: <docking sc_interface="side_chain_for_docking" minimize_water="true"/>

33: <final sc_interface="side_chain_for_final" bb_interface="backbone" minimize_water="true"/>

34: </MOVEMAP_BUILDERS>

35: 

36: <SCORINGGRIDS ligand_chain="X" width="30.0">

37: <vdw grid_type="ClassicGrid" weight="1.0"/>

38: </SCORINGGRIDS>

39: 

40: <MOVERS>

41: 

42: <Transform name="transform" chain="X" box_size="7.0" move_distance="0.1" angle="4.0" cycles="700" repeats="1" temperature="5" initial_perturb="10.0" />

------------------------------------------------------------

Warning messages were:

------------------------------------------------------------

AttachmentSize
ligand_docking.txt2.72 KB
Category: 
Post Situation: 
Mon, 2022-07-18 10:51
Delfosse57

The ligand docking on ROSIE runs in an older version of Rosetta. This means that the script as-written doesn't work for recent versions of Rosetta.

You have several options. You can either run with an older version of Rosetta (this would be about Rosetta weekly 2016.46 or Rosetta 3.7 might work), or you can run the re-writer script in tools/xsd_xrw/rewrite_rosetta_script.py on the XML, or you can just grab the most recent version of the ligand docking XML from the Meiler lab tutorials at http://csb.vanderbilt.edu/workshops/rosetta_aug2020/materials/index.php

Mon, 2022-07-18 11:22
rmoretti

Thank you so much this is very helpful!

It looks like the website is down, I will keep checking it to see if it gets brought back up soon otherwise Ill use the conversion script.

Thank you

Mon, 2022-07-18 11:33
Delfosse57

Hmm, looks like some website server settings issues. The direct link to the videos and contents for ligand docking are below:

https://www.youtube.com/watch?v=-4wgIuMfr_w&list=PLYuStm_BniykhlMFAus-UEwR-_qmAVWsK

http://staging.meilerlab.org/wp-content/uploads/2022/02/ligand_docking.zip

Mon, 2022-07-18 11:56
rmoretti