### JOB IO
#-s input.pdb
#-native native_input.pdb # if available
-out:file:scorefile score_out_snugdock.sc
-out:path:pdb models_path_out/
-out:pdb_gz # gzip models for space
-nstruct 1000 # adequate sampling

# low-res constraints (constrain alpha/tau if available)
#-constraints:cst_file kink.cst
#-constraints:cst_weight 1.0

# high-res constraints (constrain alpha/tau if available)
#-constraints:cst_fa_file kink.cst
#-constraints:cst_fa_weight 1.0

### Docking
-partners LH_A
-spin
-dock_pert 3 8

### do not filter for h3, constraint takes care of this geom
-h3_filter false

### loop modeling settings
#
# KIC

-kic_rama2b
-loops:ramp_fa_rep
-loops:ramp_rama

-kic_omega_sampling
-allow_omega_move true

-loops:refine_outer_cycles 3
-loops:max_inner_cycles 80

# CCD (exit with ptr error)
#-antibody:centroid_refine refine_ccd
#-antibody:refine refine_ccd
#-loops:outer_cycles 5

#more standard settings, for packages used by antibody_H3
-ex1
-ex2aro
#-talaris2014 true