I am studying the Rosetta "advanced protein-protein docking" tutorial (https://www.rosettacommons.org/demos/latest/tutorials/advanced_protein-protein_docking/advanced_protein-protein_docking_tutorial), but I find some confusing problems with it.
The input file pdb file for the docking command:
$>$ROSETTA3/bin/rosetta_scripts.default.linuxgccrelease @docking_full.options -nstruct 1
is 3gbm_HA_3gbn_Ab.pdb. According to the tutorial, this file is prepared by the following steps:
(1) Download the HA protein pdb file 3GBM.pdb and the antibody pdb file 3GBN.pdb from PDB.
(2) Clean and renumber the HA protein pdb file 3GBM.pdb to get 3gbm_HA.pdb which only contains chain A and B of the HA protein.
(3) Clean, trim and renumber the antibody pdb file t3GBN.pdb to get 3gbn_Ab.pdb, and fix the chain break in the structure and get 3gbn_Ab_fixed.pdb which only contains the antibody heavy and light chains.
(4) Repack the 3gbm_HA.pdb and the 3gbn_Ab_fixed.pdb to get 3gbm_HA_repacked.pdb and the 3gbn_Ab_repacked.pdb.
(5) Open prepared HA pdb file 3gbm_HA_repacked.pdb and the antibody pdb file 3gbn_Ab_repacked.pdb together with the native HA-antibody complex pdb file, align the antibody to the native HA-antibody complex, and finally the aligned antibody, and the HA protein are save as a combined structure file, the 3gbm_HA_3gbn_Ab.pdb. This pdb file is used as the input pdb file for docking procedure.
What makes me confused is the step (5). After alignment, the HA protein (3gbm_HA_repacked) and the antibody (3gbn_Ab_repacked) form a combined structure that is almost completely the same with the native HA-antibody complex. Since the input partners are already place at the position almost completely the same with the native complex, what is the meaning of the docking in this tutorial if the purpose of docking is to get the complex structure which is as identical as possible to the native complex structure?
After docking with the command:
$> $ROSETTA3/bin/rosetta_scripts.default.linuxgccrelease @docking_full.options -nstruct 1
I get a docked complex structure, 3gbm_HA_3gbn_Ab_full_0001.pdb, which has a large RMSD value with the native complex structure. After minimization with the follow command:
$ROSETTA3/bin/rosetta_scripts.default.linuxgccrelease @input_files/docking_minimize.options -nstruct 10
I get 10 minimized complex structures. Then, I use the following command to calculates the RMSD between these minimized structures and the native complex:
$>$ROSETTA3/bin/rosetta_scripts.default.linuxgccrelease @docking_analysis.options -in:file:s *full*pdb *minimize*pdb
However, the following message is thrown out and not result file (docking_analysis.csv) is generated :
protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ...
protocols.jd2.JobDistributor: Parser is present. Input mover will be overwritten with whatever the parser creates.
protocols.jd2.JobDistributor: no more batches to process...
protocols.jd2.JobDistributor: 21 jobs considered, 0 jobs attempted in 0 seconds
protocols.jd2.JobDistributor: no jobs were attempted, did you forget to pass -overwrite?
Could anyone tell me how to solve there problems?