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protocols.jd2.JobDistributor: [ ERROR ]

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protocols.jd2.JobDistributor: [ ERROR ]

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!


Post Situation: 
Thu, 2019-04-11 09:30

Hey Johnny!


Can you include the full output here?  I've never seen an error like this before. 

Thu, 2019-04-11 09:33

Make sure to include the -nstruct option.

Thu, 2019-04-11 09:40

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/

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/
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!

Sat, 2019-04-13 07:01

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_zero_occupancy false

-load_PDB_components false




Mon, 2019-04-15 10:56

This has been fixed in a branch and will be available in the next weekly release of Rosetta. 

Tue, 2019-04-16 09:15