molclaw-fix-pdb

What problem does it solve?

This Skill automates the repair and cleaning of PDB structures using PDBFixer, producing a repaired file and topology counts to support downstream modeling and simulation workflows.

Core Features & Use Cases

• Repair broken or incomplete PDB structures and optionally add hydrogens, model missing residues, and clean heterogens or waters.
• Return the repaired PDB path plus simple topology counts (atoms, residues, chains) for verification and reproducibility.
• Use case: prepare a protein-ligand complex for MD simulation by ensuring a valid geometry and complete topology before running simulations.

Quick Start

Upload the PDB file and run the fix_pdb tool to generate a repaired PDB along with topology counts.