Noora

You need to use two more falgs alongside -xr, which are -xn and -xp flags. `obabel 3rtn.pdb -xr -xn -xp -O 3rtn.pdbqt` Here is a link to formatting options: https://open-babel.readthedocs.io/en/latest/FileFormats/AutoDock_PDBQT_format.html

can you please attach the video link? or the script they used?

You can compile Rosetta (not pyRosetta) and run simple_cycpep_predict app. Here is its documentation: https://www.rosettacommons.org/docs/latest/structure_prediction/simple_cycpep_predict

Can you share the command line?