#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_extended

#packing options; these settings are about as high as it can go before you'll hit memory problems in design mode
-ex1
-ex2
#use_input_sc does NOT maintain the input sidechain in benchmarking; it does allow maintenance of minimized sidechains between packing runs
-use_input_sc
-extrachi_cutoff 8
#for benchmarking only
-packing::repack_only
#useful if the number of rotamers is overlarge; meaningless in benchmarking w/no design
#-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
	-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

#these are used specifically to activate benchmarking
-AnchoredDesign
	-rmsd true
	-testing::delete_interface_native_sidechains true


#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