Some problems with the “advanced protein-protein docking” tutorial

[Anonymous]

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. 

Problem 1

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? 

Problem 2

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?

 

Best regards,

Yeping Sun

 

 

 

 

 

[Anonymous]

“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? “

First, using easy problems makes for better tutorials than hard problems.  Second, this makes it easy to see if the results are “right”, since they can just be overlain on the starting structure.

 

“

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?”

Did you do the command more than once?  Are the results already present on disk?  Usually this error means that Rosetta detects that whatever structures you are trying to write are already there.  This might occur if you accidentally use the same input set and output location as some earlier command.

You can always make a deep copy of the whole setup and pass -overwrite as it suggests to see what, if any, outputs you get.

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