(New user to Rosetta, so I apologize if this is the wrong place to post this or a silly question)
I am trying to use the Surface Docking application (https://www.rosettacommons.org/docs/latest/application_documentation/docking/surface-docking) to dock a protein to a crystal surface using only a fasta sequence file.
I start by making fragments (which I believe are required by surface_docking) with the fragment_picker application (https://www.rosettacommons.org/manuals/archive/rosetta3.4_user_guide/dc/d10/app_fragment_picker.html) using the following flags file:
-frags::frag_sizes 9 3
I use the command "fragment_picker.linuxgccrelease @flags" and this proceeds without error. Then I run the surface_docking application.
Here I am using the following flags file with the command "surface_docking.linuxgccrelease @flags":
This gives the following error:
> protocols.SurfaceDocking.SurfaceDockingProtocol: Loading Fragment 9:
> Open failed for file:
> ERROR:: Exit from: src/core/fragment/ConstantLengthFragSet.cc line: 155
This seems to indicate some kind of problem with the fragment files, but I don't know what the issue is. I would like to avoid using the Robetta server for fragement generation as I need to do this relatively quickly. I have also tried the fragment_picker demo and the surface_docking demo, which both completed successfully, so it is not an installation issue. The link to the fragement_picker tutorial also appears to be broken (https://www.rosettacommons.org/demos/latest/create/tutorials/denovo_structure_prediction/tutorial%20for%20fragment%20picking)
Any hep would be appreciated.