Problem with Scoring function and PlaceStub mover

[Anonymous]

Hi everyone,

I am using PlaceStub application (https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/Movers/movers_pages/PlaceStubMover) for placing two sets of different stubs on the scaffold.

1- I got following errors, although I have checked scoring function (like ref2015, beta_nov16 and score12). Furthermore, I have cleaned all pdbs to be compatible with rosetta, but again same errors. Please can somebody go through this error?

2- I am not sure about the correctness of scoring function I have put in the XML file. It would be great if someone look at scoring section as well.

FYI, I have attached XML and command files in the attachment.

 

protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER PlaceStub – place_phe_hr2=======================

core.pack.task: Packer task: initialize from command line()

core.scoring.ScoreFunctionFactory: SCOREFUNCTION: beta_nov16.wts

core.pack.pack_rotamers: built 9 rotamers at 9 positions.

core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph

core.pack.interaction_graph.interaction_graph_factory: IG: 17924 bytes

core.chemical.ResidueType: [ ERROR ] atom name : CD2 not available in residue ALA

core.chemical.ResidueType: [ ERROR ] ‘ N  ‘ 0x8002a18

core.chemical.ResidueType: [ ERROR ] ‘ CA ‘ 0x8002e68

core.chemical.ResidueType: [ ERROR ] ‘ C  ‘ 0x80039d8

core.chemical.ResidueType: [ ERROR ] ‘ O  ‘ 0x8003f58

core.chemical.ResidueType: [ ERROR ] ‘ CB ‘ 0x80042d8

core.chemical.ResidueType: [ ERROR ] ‘ H  ‘ 0x80047e8

core.chemical.ResidueType: [ ERROR ] ‘ HA ‘ 0x8004b88

core.chemical.ResidueType: [ ERROR ] ‘1HB ‘ 0x8004f28

core.chemical.ResidueType: [ ERROR ] ‘2HB ‘ 0x80052c8

core.chemical.ResidueType: [ ERROR ] ‘3HB ‘ 0x80059f8

core.chemical.ResidueType: [ ERROR ]

protocols.protein_interface_design.movers.PlaceStubMover: switching interface to alanine

DEBUG.PlaceStubMover: removed 29 bb constraints from pose

before removal 165 after removal 136

protocols.rosetta_scripts.ParsedProtocol: [ ERROR ] Exception while processing procotol:

protocols.jd2.JobDistributor: [ ERROR ]

[ERROR] Exception caught by JobDistributor for job anti.patchdock.1_0246

[ ERROR ] EXCN_utility_exit has been thrown from: src/core/chemical/ResidueType.cc line: 3807

ERROR: unknown atom_name: ‘CD2’  in residue ALA

protocols.jd2.JobDistributor: [ WARNING ] anti.patchdock.1_0246 reported failure and will NOT retry

 

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