Hi I met the error "protocols.jd2.JobDistributor: [ ERROR ] " when I run antibody_designer of RAbD, that I tried to use 3ogo.pdb (renumbered with PyIgClassify), which is a nanobody-antigen complex structure, as input.
Has anyone come across the same error before?
My command was:
/home/cltam/Desktop/rosetta_bin_linux_2018.33.60351_bundle/main/source/bin/antibody_designer.static.linuxgccrelease -s 3ogoOut.pdb -primary_cdrs H3 -graft_design_cdrs H3 -seq_design_cdrs H1 H2 -allow_omega_mismatches_for_north_clusters
Thanks in advance!
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Post Situation:
Hey Johnny!
Can you include the full output here? I've never seen an error like this before.
Make sure to include the -nstruct option.
I used the following command:
/home/cltam/Desktop/rosetta_bin_linux_2018.33.60351_bundle/main/source/bin/antibody_designer.static.linuxgccrelease -s both-prepwizarded_remove-ACE-NMA.pdb -primary_cdrs H3 -graft_design_cdrs H3 -seq_design_cdrs H1 H2 -allow_omega_mismatches_for_north_clusters -nstruct 10
Which gave me the following error message with highlight (other than as shown, no other errors appeared):
...
antibody.AntibodyInfo: Setting up CDR Cluster for H1
protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT
antibody.AntibodyInfo: Setting up CDR Cluster for H2
protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTTTT
antibody.AntibodyInfo: Setting up CDR Cluster for H3
protocols.antibody.cluster.CDRClusterMatcher: Length: 15 Omega: TTTTTTTTCTTTTTT
protocols.antibody.clusters.CDRClusterSet: Adding cacheable cluster data to pose
protocols.antibody.NativeAntibodySeq: Setting full pose sequence
protocols.jd2.JobDistributor: [ ERROR ]
[ERROR] Exception caught by JobDistributor for job both-prepwizarded_remove-ACE-NMA_0001
File: src/protocols/antibody/AntibodyInfo.cc:1117
L1 start resnum not found in pose: 24 L
Please check pdb is renumbered properly and the passed -numbering_scheme option matches the PDB.
This could also mean missing density in the cdr loop. Loop modeling applications can be used to fill missing residues
protocols.jd2.JobDistributor: [ ERROR ]
protocols.jd2.JobDistributor: [ WARNING ] both-prepwizarded_remove-ACE-NMA_0001 reported that its input was bad and will not retry
protocols.jd2.FileSystemJobDistributor: job failed, reporting bad input; other jobs of same input will be canceled: both-prepwizarded_remove-ACE-NMA_0001
protocols.jd2.JobDistributor: no more batches to process...
protocols.jd2.JobDistributor: 10 jobs considered, 1 jobs attempted in 2 seconds
Error: [ ERROR ] ERROR: Exception caught by antibody_design application:
File: src/protocols/jd2/JobDistributor.cc:329
1 jobs failed; check output for error messages
Although I have already used schrodinger prepwizard to fill loops for both my antibody (already renumbered with PyIgClassify) and antigen, I still got the same error message.
Do you have any idea what happened?
Thank you!
Hey Johnny,
Can you send me an email with the inputs? I'll try this locally and try to see what the problem is . Can you also try with these options? I use these for most of my work in Rosetta:
-ignore_unrecognized_res
-ignore_zero_occupancy false
-load_PDB_components false
Thanks,
-Jared
This has been fixed in a branch and will be available in the next weekly release of Rosetta.