I have an 18 subunit, helical enzyme that I'm trying to make more stable. I have, however, truncated it to include only one of each interacting surface.
I've tried pmut scan, and it predicted mutations at the core. The issue is that it isn't predicting specific mutations at the interfaces, the part of the protein that I know contributes significantly to the enzyme's stability. When I try to run pmut_scan on anything more complex than the dimer subunit I get this error ERROR: Error in core::conformation::Conformation::residue(): The sequence position requested was 0. Pose numbering starts at 1.
I tried to solve this using a symmetry definition file but when I run pmut_scan with the file as input, I get the same error.
Then I saw on the forum that some Rosetta applications inlcuding pmut_scan aren't designed to accept symmetry definition files and that an option would be to use OptGreedyMutationMover. I've looked on the version of rosetta that I have (3-.12) and I can't seem to find a template or example of the script or a demo.
I would appreciate help of any kind on how to get Rosetta to recognise the interfaces and predict possible point mutations that potentially contribute to an overall lower enenrgy for the whole protein.