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!
I don't know why it's not outputting. Try removing your output override flags and it will just dump outputs to the directory you ran in.
I do think you need those constraints. I don't know how to make them, but the enzyme design documentation should.
I can see from your log file that a residue X is getting completely ignored because it has zero occupancy - the log file tells you how to fix that if you want to.
You're running at nstruct 1, which is appropriate for debugging, but do remember to turn that setting up once it's working!
My initial gut impression is that the file you're specifying for output can't be opened for writing by Rosetta. Does the directory (/home/qgem/Documents/pdbs) exist with the appropriate permissions? You may want to try a test run omitting the -out:path options and writing to the current directory to see if those settings are causing you issues.
The reason you're only getting one attempted output structure is because you're using the default -nstruct of 1. Increase that value to get more output structures.
You should be able to run enzdes without the constraints, although if you have key interactions you want to preserve, it may be beneficial to add them. See https://www.rosettacommons.org/docs/latest/rosetta_basics/file_types/match-cstfile-format for details on the format, and look at the demos/public/enzyme_design/ for an example of usage.