drug-complex-system-builder

Goal

To take a prepared protein (PDB) and a validated ligand pose (SDF) and produce a fully parameterized, solvated, ion-neutralized OpenMM simulation bundle ready for drug-protein-ligand-md.

The output bundle includes:

• Serialized OpenMM System XML (force field parameters, constraints)
• Full-precision initial state XML (positions + box vectors for exact restart)
• Solvated PDB with protein + ligand + water + ions (for visualization)
• Provenance JSON recording all build parameters

Instructions

1. Prepare inputs

Required inputs:

• Receptor PDB: from drug-protein-prep (protonated, missing residues resolved).
• Ligand SDF: from drug-pose-validation or drug-docking-vina. Must have 3D coordinates in the receptor frame and explicit hydrogens.