Abstract
<jats:p>Preparing molecular dynamics (MD) systems for cytochrome P450 (CYP) complexes is error-prone because experimental coordinates, heme-state-specific parameters, proximal cysteinate coordination, ligand chemistry, partial charges, and topology definitions must be reconciled across incompatible representations. CYPForge formulates this task as an auditable chemical-information assembly contract: three modules reconstruct IC6, DIOXY, or Compound I heme–thiolate geometries, map SDF-defined ligand chemistry onto PDB binding poses before GAFF2/RESP parameterization, and assemble solvated AMBER systems under fail-fast checks for identity, charge, protonation decisions, connectivity, and topology read-back; an optional Outer Shell restricts LLM-assisted execution to manifest-authorized operations. Across 10 test cases spanning multiple heme states, CYP isoforms, and ligand chemotypes, seven ligand-bound 100-ns trajectories showed structural retention; agent-ablation endpoint completion was 9/9 with the full workflow, 8/9 without the Outer Shell, and 0/9 without CYPForge. CYPForge replaces fragmented cross-tool preparation with a traceable, restartable workflow while preserving expert control over heme-state assignment, protonation, and interpretation; the MIT-licensed software is available at https : //github.com/ZiyanZhuang/CYPForge.</jats:p>