I tried to dock the protein and DNA or RNA with perturbation flags, everything seems going well, but at the end of the docking, these is no output pdb files. Below is the information at the end of the log file, and also the flags are shown.
protocols.docking.DockingProtocol: Scoretype: interchain_contact score: 12, cutoff: 9.99
protocols.docking.DockingProtocol: Scoretype: interchain_vdw score: 0, cutoff: 1
protocols.jd2.FileSystemJobDistributor: Too many retries (max_retry_job = 10)
protocols.jd2.JobDistributor: 10MH_0001 reported failure and will retry
protocols.jd2.JobDistributor: no more batches to process...
protocols.jd2.JobDistributor: 1 jobs considered, 11 jobs attempted in 66 seconds
-dock_pert 3 8
If I change the perturbation flag "-dock_pert 3 8" to refinement flag "-docking_local_refine", it works well and the pdb file is produced. How to deal with this problem? your response and help is very appreciated.