#database path
#-database /path/to/database

#altering output
#mute at your choice
#-mute core.chemical core.scoring.etable core.io.database core.io.pdb.file_data core.conformation core.pack.pack_rotamers core.pack.task
-unmute protocols.loops.CcdLoopClosureMover

#repeating options for safety
-run::version
-options::user

#input files
-s 1zr0.CD.pdb
-loops::loop_file loopsfile_native

#packing options - these are about as high as they can go
-ex1
-ex2
-use_input_sc
-extrachi_cutoff 8
-resfile resfile
-linmem_ig 42

#minimization options
-run::min_type dfpmin_armijo
-nblist_autoupdate

#useful in MPI, depending on how you choose to run it
#-mpi_work_partition_job_distributor
#-mpi_tracer_to_file proc

#loops options
-loops::vicinity_sampling true

#AnchoredDesign options
-AnchoredDesign
	-anchor anchor
	-allow_anchor_repack false
	-vary_cutpoints true
	-debug false
	-show_extended false
	-refine_only false
	-perturb_show false
	-perturb_temp 0.8 
	-refine_temp 0.8
	-refine_repack_cycles 50
	-rmsd false
	-unbound_mode false
	-no_frags false
	-perturb_CCD_off false
	-perturb_KIC_off false
	-refine_CCD_off false
	-refine_KIC_off false
	-chainbreak_weight 2.0
	-testing::VDW_weight 2


#no filters


#production command
#-AnchoredDesign::perturb_cycles 5000
#-AnchoredDesign::refine_cycles 10000
#-nstruct 9999

#sample-size command
-AnchoredDesign::perturb_cycles 50
-AnchoredDesign::refine_cycles 100
-nstruct 4