config_20260213_105001.yaml

# ==============================================================================
# Colbuilder Configuration - Topology Generation Only
# ==============================================================================
# This configuration generates topology files from an existing fibril PDB file
# without performing sequence generation, geometry generation, or mixing.
# ==============================================================================

# Operation Mode
mode: null
config_file: null
sequence_generator: false     # No sequence generation
geometry_generator: false     # No geometry generation
topology_generator: true      # Only generate topology files
debug: false

# Species Configuration
species: "rattus_norvegicus"  # Species identifier for output naming

# Input PDB File
# IMPORTANT: Provide the path to your existing mixed fibril PDB file
pdb_file: "collagen_fibril_rattus_norvegicus_MIX.pdb"

# Sequence Settings (Not used in topology-only mode, but required fields)
fasta_file: null
crosslink: true
n_term_type: "PYD"
c_term_type: "PYD"
n_term_combination: "6.B - 9.C - 946.A"
c_term_combination: "1046.C - 1046.A - 103.C"

# Geometry Parameters (Not used in topology-only mode, but may be required fields)
contact_distance: 30
fibril_length: 80.0
crystalcontacts_file: null
connect_file: null
crystalcontacts_optimize: false

# Mixing Options (Disabled for topology-only mode)
mix_bool: false
ratio_mix: "A:70 B:30" 
files_mix:                   # Required if mix_bool is true
 - "rattusnorvegicus_N_PYD_C_PYD.pdb" # PDB file of collagen molecule with type A crosslinks (created by only setting squence and crosslinks = true (please look at the examples))
 - "rattusnorvegicus_N_HLKNL_C_HLKNL.pdb" # PDB file of collagen molecule with type B crosslinks

# Replacement Options (Disabled for topology-only mode)
replace_bool: false
ratio_replace: null
replace_file: null

# Topology Options
force_field: "amber99"        # Force field for topology generation
                              # Options: "amber99" or "martini3"
topology_debug: false         # Keep intermediate topology files for debugging