protocols.jd2.JobDistributor: [ ERROR ]

[Anonymous]

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!

 

[Anonymous]

Hey Johnny!

 

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

[Anonymous]

Make sure to include the -nstruct option.

[Anonymous]

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!

[Anonymous]

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

[Anonymous]

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

[Author]

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