I've been trying to run the enzyme design application with the purpose of optimizing an enzyme binding pocket that normally binds phenylalanine, to increase its affinity to bind leucine instead. I am running the application with leucine already docked in the binding pocket and with specified residue positions, which I know from literature control this enzyme's ligand specificity. I do not have a CST file as I don't know how to create one properly, and I was hoping that since my enzyme came from a proper crystal structure that I may not need to.
The issue is that, as seen in the terminal output, the application only creates 1 structure before quitting (dockedDomain2_0001), and said structure is not saved as output in any way, it's nowhere to be found. I have attached my outputs and command options if they help. I am very very new to Rosetta so I'm sorry for the fairly broad question, but I can't identify the source of the issue with my run.
Any advice would be much appreciated!