I am new to Rosetta and was trying Protein-Protein Docking tutorial. I was about to run a local docking but it gives me an error saying that
"ERROR: Cannot open file "input_files/col_complex.pdb"
so when I checked the "flag_local_docking" file there is a file called col_complex.pdb needed as input. But I don't understand how to build this file.
This is simply the structures of the two protein partners you wish to dock, combined into a single PDB file. For local/refinement docking, you want to make sure that the two binding partners are oriented with respect to each other in the general location they will be when they are bound. The local docking will refine this orientation, but will not make big changes in the global orientation of these two proteins. If you wish to have Rosetta search for the best relative orientation of the two proteins, you'll want to do global docking instead.