-in
	-file
		-s Glycoprotein-with-water.pdb
		-extra_res_fa lig.params
		-load_PDB_components false
# 		-treat_residues_in_these_chains_as_separate_chemical_entities "W"
#		-native Glycoprotein-with-water.pdb
	-ignore_waters false
	-auto_setup_metals true
	-metals_detection_LJ_multiplier 1.0
	-metals_distance_constraint_multiplier 1.0
	-metals_angle_constraint_multiplier 1.0
	-include_sugars true
	-alternate_3_letter_codes pdb_sugar.codes
	-auto_detect_glycan_connections true
	-maintain_links true
	-min_bond_length 1.1
	-max_bond_length 1.7
	-detect_disulf true
	-detect_disulf_tolerance 1.0

-overwrite

-corrections
	-beta_nov16 true
	-water
		-water_bump_check true
		-lkb_overlap_distance 0.75
		-lkb_cluster_radius 1.0
		-lkb_rotset_radius 3.0
		-dwell_cutoff 0.02
		-cluster_radius 1.52
		-cluster_cutoff 0.179
		-wat_axis_sampling true

-hydrate
	-hydrate_all true		
	-force_enforce_all_waters true
	
-relax
	-use_explicit_water true

-run
	-output_hbond_info
	-ignore_zero_occupancy false
#	-show_simulation_in_pymol 1
	
#-keep_pymol_simulation_history true

-out
	-suffix _cd
	-nstruct 1
	-file
		-write_glycan_pdb_codes true
		-write_pdb_link_records true
#		-use_pdb_format_HETNAM_records true
		-renumber_pdb false
#		-no_chainend_ter true
#		-output_virtual false
#		-output_virtual_zero_occ false
#		-suppress_zero_occ_pdb_output true
# 	-scorecut 0.5

-parser
	-protocol CM.xml

-database  ~/rosetta_src_2021.16.61629_bundle/main/database/
-database  ~/rosetta.ncaa.rotamer.libraries/

-coupled_moves
	-ligand_mode true
	-number_ligands 1
	-ligand_weight 1.0
	-ligand_prob 1.0
	-backbone_mover backrub
	-ntrials 100
	-initial_repack false
	-min_pack true
	-mc_kt 0.616
	-boltzmann_kt 0.616
	-bias_sampling true
	-bump_check true
	-save_sequences false
	-exclude_nonclashing_positions false

-packing
	-ex1
	-ex2
	-ex1aro
	-ex2aro
	-use_input_sc
	-no_optH false
	-optH_MCA true
	-multi_cool_annealer 10
	-resfile 3iai.res