I build Rosetta 2015.12 on Scientific Linux 7 (SL-7). And, I follow the protocol of RosettaAntibody3 to do antibody modeling.
When, I run the script of “antibody.py” through following command as
./antibody.py --light-chain ./L_chain.fasta --heavy-chain ./H_chain.fasta --rosetta-bin /home/rosetta_2015_12/main/source/bin --rosetta-database /home/rosetta_2015_12/main/database --blast /home/ncbi-blast-2.2.30+/bin/blastp
It can run protein blast and analyze six complementarity determining regions (CDRs) of antibody’s variable region (Fv). But, Rosetta terminate with an error as
[ERROR] Exception caught by JobDistributor for job FR_0001CCDLoopClosureMover::get_anchors( core::conformation::Residue const & residue ): Residue is not a cutpoint variant! You must add cutpoint variants before applying this Mover.
protocols.jd2.JobDistributor: FR_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: FR_0001
protocols.jd2.JobDistributor: no more batches to process...
protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 5 seconds
caught exception 1 jobs failed; check output for error messages
Rosetta run terminated with Error!
Is this correct way to do antibody modeling? How should I do to solve this problem?
Thanks for your kindly help.
This has been a known issue with RosettaAntibody; however, a fix has been implemented into the Rosetta source about a week ago. Try the antibody.py script next week and you should be good to go. In the meantime, antibody modeling can be accomplished through ROSIE: http://rosie.rosettacommons.org/
Thank you for your kindly help. I will try ROSIE and new antibody.py script.