ligand_docking_error

[Anonymous]

Dear friends, 

I am a beginner of Rosetta. While I am running ligand-docking toturial (https://www.rosettacommons.org/demos/latest/tutorials/ligand_docking/ligand_docking_tutorial). I encounter an error when run script calculate_ligand_rmsd.py when doing data analysis. This script is used to calculate RMSD of each model comapred with the best model. When I run this script, the error indicated that “capture_command.sh” does not exist. and also the calculation only be done for the first nine model. When I delete “capture_command.sh”, that is the last line in the script, there is no error anymore but the calculation still was just performed for the first nine model. I am also a beginner of coding, so I would appreciate anyone could suggest me the solution.

 

 

 

[ywang345@compute-8-0 out]$ ~/tutorials-3.12/ligand_docking/scripts/calculate_ligand_rmsd.py -n 3PBL_ETQ_0003.pdb -c X -a 7 -o rmsds_to_best_modeltest2.data *_000*.pdb

file, name: 3PBL_ETQ_0003.pdb native

file, name: 3PBL_ETQ_0001.pdb docked

Doing aligning

file, name: 3PBL_ETQ_0003.pdb native

file, name: 3PBL_ETQ_0002.pdb docked

Doing aligning

file, name: 3PBL_ETQ_0003.pdb native

file, name: 3PBL_ETQ_0003.pdb docked

Doing aligning

file, name: 3PBL_ETQ_0003.pdb native

file, name: 3PBL_ETQ_0004.pdb docked

Doing aligning

file, name: 3PBL_ETQ_0003.pdb native

file, name: 3PBL_ETQ_0005.pdb docked

Doing aligning

file, name: 3PBL_ETQ_0003.pdb native

file, name: 3PBL_ETQ_0006.pdb docked

Doing aligning

file, name: 3PBL_ETQ_0003.pdb native

file, name: 3PBL_ETQ_0007.pdb docked

Doing aligning

file, name: 3PBL_ETQ_0003.pdb native

file, name: 3PBL_ETQ_0008.pdb docked

Doing aligning

file, name: 3PBL_ETQ_0003.pdb native

file, name: 3PBL_ETQ_0009.pdb docked

Doing aligning

(the script ended and only the first nine model were compared and calcualted)

[Anonymous]

 I am a beginner of Rosetta too.  whenrunning ligand-docking toturial,happen the same questions. do not how to solve it?

[Anonymous]

I dont know neither. Seems like nobody reply to me. Have you resolved it? 

[Anonymous]

I dont know neither，so far,  i can not run this modeller.

Do you solve it？？

[Author]

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