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Illegal attempt to score with non-identical atom set between pose and etable

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Illegal attempt to score with non-identical atom set between pose and etable
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Hi! I am trying to use BlueprintBuilder to design based on the blueprint file. I wrote an xml file but it reports an error: core.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree. core.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 88 BB 1 core.kinematics.AtomTree: [ WARNING ] DOF for this torsion angle could not be found in AtomTree. core.conformation.Conformation: [ WARNING ] Unable to set torsion angle in atom_tree: TorsionID 45 BB 1 protocols.forge.remodel.RemodelMover: start stop cut cbreak protocols.forge.remodel.RemodelMover: 1 22 0 0 protocols.forge.remodel.RemodelMover: 36 49 44 17.8048 protocols.forge.remodel.RemodelMover: 60 96 87 32.5301 protocols.forge.remodel.RemodelMover: 109 141 114 20.4534 protocols.forge.remodel.RemodelMover: 153 166 153 4.11535 protocols.forge.remodel.RemodelMover: 175 228 0 0

ERROR: Illegal attempt to score with non-identical atom set between pose and etable pose atom_type_set: 'centroid' etable atom_type_set: 'fa_standard'

ERROR:: Exit from: src/core/scoring/etable/EtableEnergy.cc line: 281 protocols.rosetta_scripts.ParsedProtocol: [ ERROR ] Exception while processing procotol:

File: src/core/scoring/etable/EtableEnergy.cc:281 [ ERROR ] UtilityExitException ERROR: Illegal attempt to score with non-identical atom set between pose and etable pose atom_type_set: 'centroid' etable atom_type_set: 'fa_standard'

protocols.jd2.JobDistributor: [ ERROR ]

[ERROR] Exception caught by JobDistributor for job model-0.relaxed_0003_0001_0001

[ ERROR ]: Caught exception:

File: src/core/scoring/etable/EtableEnergy.cc:281 [ ERROR ] UtilityExitException ERROR: Illegal attempt to score with non-identical atom set between pose and etable pose atom_type_set: 'centroid' etable atom_type_set: 'fa_standard'

AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS.

It seems like I am not using the right pdb but before I use the blueprintBuilder I used files in the demos/tutorials/full_atom_vs_centroid/flag_from_fa_to_cen to change my pdb into the centroid representation mode and it worked successfully. The attached file is my xml file. Could anyone please help me to solve this problem? Thank you!

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Fri, 2024-06-07 03:22
ng98

There's two major types of score functions in Rosetta, corresponding to the two major types of Pose representation.

Most activities in Rosetta work with the "full atom" representation, and thus would use a full atom scorefunction. However, there are certain sub-protocols which work with a simplified reduced-atom representation known as "centroid mode". (So called because the main feature is that the sidechains are represented by a single "centroid" super-atom, rather than by all the atoms.) In order to properly score a centroid pose, you need to have a centroid scorefunction. (That is, a score function which has terms which work with the centroid representation of the structure.)

BluePrintBDR is one of those Movers which works with a centroid representation, and the "scorefxn" you pass to the tag should be a centroid scorefunction.

The default scorefunction used is "fldsgn_cen". You can either use this the weights in your scorefunction tag, or you can probably just omit the `scorefxn` option from the BluePrintBDR tag -- if you don't specify a scorefunction, it will use that one by default.

Fri, 2024-06-07 06:58
rmoretti