# List of refined models to compare RMSD to
-in:file:l models.ls	

# Native structure for RMSD calculation
-in:file:native 1AFO_tr_AB.pdb	

# Use hi-res membrane score function 
-score:weights mpframework_smooth_fa_2012	

# Input is a membrane protein
-in:membrane	

# Read membrane residue at position 327
-mp:setup:membrane_rsd 81	

# Input spanfile
-mp:setup:spanfiles 1AFO_tr_AB.span	

# Turn on membrane hydrogen bonding
-mp:scoring:hbond	

# Wait to pack sidechains until membrane is present
-packing:pack_missing_sidechains 0	
