config_replace.yaml

# Replacement Options (for fewer crosslinks)

species: "homo_sapiens"  
fasta_file: null             # Custom FASTA file path (if null, auto-generated based on species)
crosslink: true              # Enable crosslinking in the model
n_term_type: "HLKNL"         # N-terminal crosslink type (Options: "DPD", "DPL", "HLKNL", "LKNL", "PYD", "PYL", "deHHLNL", "deHLNL", "NONE") 
c_term_type: "HLKNL"         # C-terminal crosslink type (Options: "DPD", "DPL", "HLKNL", "LKNL", "PYD", "PYL", "deHHLNL", "deHLNL", "NONE")
n_term_combination: "9.C - 947.A"    # N-terminal residue combination
c_term_combination: "1047.C - 104.C" # C-terminal residue combination

working_directory: "./"
replace_bool: true          # Enable crosslink replacement
ratio_replace: 30            # Percentage of crosslinks to replace
replace_file: "collagen_fibril_homo_sapiens.pdb"            # File with crosslinks to be replaced (set to null if geometry_generation is true)

# Topology Options
force_field: "amber99"