I'm trying to dock a protein with an ssDNA using the full protocol flags :
But, I obtain the message error :
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: HBsAg_Aptamer_0001_0001 reported failure and will retry
protocols.jd2.JobDistributor: no more batches to process...
protocols.jd2.JobDistributor: 1 jobs considered, 11 jobs attempted in 68 seconds
Can anyone know the solution to overpass this problem and realize the docking protocol protein/ssDNA ?
It's a known limitation of the Rosetta Docking protocol that it can't handle protein-nucleic acid complexes - at least not to the same extent that it can protein-protein complexes. The issue is that the protocol starts with a low-resolution general stage. The scoring function it uses in that stage is protein-specific, and results in zero energies for the nucleic acid partner. This means that the interface energies are all computed as zero, leading to filter failures.
You can do high-resolution refinement of protein-nucleic acid complexes, but not the low-resolution search stage.
There are people currently working on protein-nucleic acid docking protocols, but there isn't anything finished with that, yet.