I am trying to run the initial_assignment using auto noe. When I run the command, I get the following error:
ERROR: ERROR: Option matching -chemical:patch_selectors not found in command line top-level context
How do I fix it?
What version of Rosetta are you using? My guess is that you're using an older version, one which doesn't support the -chemical:patch_selector syntax.
I'd highly recommend updating to a more recent version of Rosetta (e.g. Rosetta 3.8).