config_ex1.yaml

mode: null
config_file: null
sequence_generator: true
geometry_generator: true
topology_generator: true 
debug: false

# Input Configuration
species: "homo_sapiens"

# Sequence Settings
fasta_file: null
crosslink: true
n_term_type: "HLKNL"
c_term_type: "HLKNL"
n_term_combination: "9.C - 947.A"
c_term_combination: "1047.C - 104.C"

# Geometry Parameters
pdb_file: null
contact_distance: 20
fibril_length: 60.0
crystalcontacts_file: null
connect_file: null
crystalcontacts_optimize: false

# Mixing Options
mix_bool: false
ratio_mix: "A:70 B:30"       # Format: "Type:percentage Type:percentage"
#files_mix:                   # Required if mix_bool is true
# - "collagen-molecule-crosslinkA.pdb" # PDB file of collagen molecule with type A crosslinks (created by only setting squence and crosslinks = true (please look at the examples))
# - "collagen-molecule-crosslinkB.pdb" # PDB file of collagen molecule with type B crosslinks
# Replacement Options
replace_bool: false

# Topology Options
force_field: "amber99"