PDBDNAConv: A software suite for generating atomistic DNA geometries for Geant4-DNA Monte Carlo simulations from Protein Data Bank (PDB) structures

Accurate simulation of radiation-induced DNA damage requires geometry models that preserve atomic structure while satisfying Geant4-DNA constraints. We present PDBDNAConv, a modular software suite that provides an automated pipeline for converting Protein Data Bank (PDB) structures into simulation-ready geometries. The software reconstructs hierarchical DNA models based on atomic structure using ellipsoidal approximation categorized for sugar, phosphate, and base moieties in nucleotide to reduce geometric complexes. Geometric overlaps are automatically detected and resolved to ensure valid geometry construction. Structured output is serialized in JSON format for interoperability and seamless integration into Geant4-DNA simulations. The exported JSON files are loadable by an example Geant4-DNA application through developed geometry construction classes that enable atomic-scale analysis of direct and indirect DNA damage.