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config.yaml
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config.yaml
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# Operation Mode
# Note: These are typically set automatically based on other flags
mode: null # Can be a combination of SEQUENCE, GEOMETRY, TOPOLOGY, FIBRIL, MIX, REPLACE
# General Configuration
config_file: null # Path to this YAML configuration file
debug: false
# Sequence Generation Configuration
sequence_generator: true
fasta_file: homosapiens.fasta
output_prefix: "my_collagen_sequence"
species: "Homo_sapiens"
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 Generation Configuration
geometry_generator: true
file: null #homosapiens_N_HLKNL_C_HLKNL.pdb # Input PDB file. Note: Comment this line if sequence_generator is true
output: "collagen_fibril"
working_directory: "./"
contact_distance: 60
fibril_length: 334.0
crystalcontacts_file: null # crystalcontacts_from_colbuilder.txt
connect_file: null
crystalcontacts_optimize: false # Note: This is always true when generating geometry from contact_distance, but has to be set to true to be performed otherwise.
# Mix Configuration
mix_bool: false
ratio_mix: "D:70 T:30"
files_mix:
- "human-D.pdb" # D: divalent
- "human-T.pdb" # T: trivalent
# Replace Configuration
replace_bool: false
ratio_replace: 30
replace_file: null
# Topology Generation Configuration
topology_generator: false
force_field: amber99 # Note: Choose between "amber99" and "martini"