
# this is to set the initial centroid coordinate for the ligand starting position. 
-parser:script_vars startfrom=./protein_files/1kv2_startfrom.pdb

# -ex1 and -ex2 expand then sampling of rotamers in the first 2 chi angles of protein sidechains to improve the quality of packing
-ex1 
-ex2 

# The RosettaLigand scoring functions do not use the new functionality of the talaris_2013 scoring function. This flag is required to turn off those functions
-restore_pre_talaris_2013_behavior true

# The benchmarking study in the manuscript used 2000 models for each protein-ligand complex.
# -nstruct is set to 10 because in this example, but normally this would be increased depending on how many ligands/protein complexes you are looking at.
-nstruct 2

# output PDB files for viewing in pymol
-out:pdb
