The structures that I'm generating with Rosetta are missing the hydroxyl group at the C terminus. I'm guessing this is because the residues are generated without them so that they can be connected to one another, but this is creating problems for me when I try to analyze the generated structures.
How can I run Rosetta in a way that will cap the C terminus correctly? Is there a specific option? Or a separate command? Here's the main command in what I'm running:
"rosetta aa inpu _ -relax -farlx -termini -minimize -s highRes -fa_input -fa_output > refine.log"
When I look at files from the PDB, they have something similar to this line at the C terminus, which is the OH group:
"ATOM 2590 OXT SER B 416 48.151 19.779 122.824 1.00107.18 O"
Any help would be greatly appreciated; thanks!