Here's the source code of mutation_script.xml, part of the demo calculate_protein_protein_ddg included in Rosetta (see https://www.rosettacommons.org/demos/latest/public/calculate_protein_protein_ddg/README). I deleted the comments to make it shorter:
<dock_design> <SCOREFXNS> </SCOREFXNS> <FILTERS> <Ddg name=dg_wt threshold=1000 repeats=3 jump=3/> <Ddg name=dg_mut threshold=1000 repeats=3 jump=3/> </FILTERS> <TASKOPERATIONS> <RestrictToRepacking name=repack_only /> <ReadResfile name=resfile filename=UbcH7-A98W.resfile/> </TASKOPERATIONS> <MOVERS> FastRelax name=relax/> <PackRotamersMover name=pack task_operations=repack_only/> <PackRotamersMover name=mut_and_pack task_operations=resfile/> </MOVERS> <PROTOCOLS> Add mover_name=relax/> <Add mover_name=pack/> <Add filter_name=dg_wt/> <Add mover_name=mut_and_pack/> <Add filter_name=dg_mut/> </PROTOCOLS> </dock_design>
You can see that the FastRelax mover is commented out (it's missing the opening <). This is exactly like this on the original mutation_script.xml file included in Rosetta.
Is this a typo or is there a reason for this? Note that I don't care so much for computation time. I want to obtain results as accurate as possible. So what is the recommended protocol here? Use FastRelax or not?