#protocol called in RosettaScripts
-parser:protocol mp_relax.xml

#PDB input file
-in:file:s 1afo_tr_AB.pdb

#span input file
-mp:setup:spanfiles 1afo_tr_AB.span

#include hydrogen bond correction in scoring
-mp:scoring:hbond 

#create 3 output models
-nstruct 3

#run FastRelax protocol
-relax:fast

#move the membrane with respect to the protein
-relax:jump_move true

#output PDB files instead of silent files
-out:pdb

#specify output filename for scoring
-out:file:scorefile mp_relax_scores_1afo.sc

#do not pack sidechains until the membrane is added
-packing:pack_missing_sidechains 0
