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Graylab / deepH3-distances-orientations

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There is something wrong when I use deeph3 constrains in rosetta. #6

Open alexpadholol opened 3 years ago

alexpadholol commented 3 years ago

Log as below:

core.scoring.constraints.ConstraintsIO: [ ERROR ] reading of AtomPair failed.

ERROR: [ ERROR ]reading of AtomPair failed.

ERROR:: Exit from: src/core/scoring/constraints/ConstraintIO.cc line: 559 protocols.rosetta_scripts.ParsedProtocol: [ ERROR ] Exception while processing procotol:

File: src/core/scoring/constraints/ConstraintIO.cc:559 [ ERROR ] UtilityExitException ERROR: [ ERROR ]reading of AtomPair failed.

protocols.jd2.JobDistributor: [ ERROR ]

[ERROR] Exception caught by JobDistributor for job model-0_0001

[ ERROR ]: Caught exception:

File: src/core/scoring/constraints/ConstraintIO.cc:559 [ ERROR ] UtilityExitException ERROR: [ ERROR ]reading of AtomPair failed.

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

protocols.jd2.JobDistributor: [ WARNING ] model-0_0001 reported failure and will NOT retry protocols.jd2.JobDistributor: no more batches to process... protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 8 seconds

[ ERROR ]: Error(s) were encountered when running jobs. 1 jobs failed; Check the output further up for additional error messages.

heiidii commented 3 years ago

Alex, could you provide more details? How did you obtain the constraints? And how are you running Rosetta -- which application, flags etc. The most common reason for constraints to fail is a mismatch between the fasta/pdb file that was used to generate the constraints and the pdb file that is used to run Rosetta. For example, residues that are missing in pdb but present in fasta will trigger an error as the atom-pair constraints will not match up with the residues in the Rosetta pose.

alexpadholol commented 3 years ago

Thanks，there is a mismatch between fasta and pdb.