I am using the antibody.py script that comes with PyRosetta (rosetta_src_2016.13.58602_bundle, v3.6) and associated software to generate structural models for VH/VL sequences. For most of the sequences that I am using as input, the script terminates at the antibody_graft step with an error (pasted below):
Error: ERROR: Exception caught by JobDistributor while trying to get pose from job 'FR0_0001'
Error: Cannot normalize xyzVector of length() zero
Error: Treating failure as bad input; canceling similar jobs protocols.jd2.FileSystemJobDistributor: job failed, reporting bad input; other jobs of same input will be canceled: FR0_0001 protocols.jd2.JobDistributor: no more batches to process... protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 2 seconds caught exception 1 jobs failed; check output for error messages
When I examine the input file (generated in previous steps and called FR0.pdb), the only thing that is in common for all input sequences that fail here is that there are main-chain atoms inserted that have been given numbers and coordinates like in the example excerpt:
ATOM 0 CA THR L 30A 189.954-268.030-229.397 1.00 25.00
ATOM 0 CA SER L 30B 191.164-270.358-231.659 1.00 25.00
ATOM 0 CA ALA L 30C 192.374-272.686-233.921 1.00 25.00
ATOM 0 CA TYR L 30D 193.584-275.014-236.183 1.00 25.00
ATOM 0 CA PHE H 100B 544.800-310.561 442.751 1.00 25.00
These atoms lie on straight lines far away from the protein chain and represent "inserted" residues into the CDR loops.
When I remove those lines from the FR0.pdb, save the file as FR0_test.pdb, and run it through the procedure that fails above (antibody_graft), the procedure runs normally with a successful exit state.
Despite the normal run, the fact is that the removed amino acids do belong in the CDR loops and removing them is wrong.
I would appreciate any help!
Best regards, thanks in advance,