drug-complex-system-builder

What problem does it solve?

This Skill builds a complete, solvated, charge-neutralized protein–ligand complex suitable for OpenMM molecular dynamics from a prepared receptor structure and a validated ligand pose.

Core Features & Use Cases

• OpenMM System Bundle Generation: Produces serialized OpenMM system.xml plus a full-precision state_initial.xml for exact restart.
• Ligand + Protein Parameterization: Uses Amber ff14SB for the protein and OpenFF Sage (or GAFF with AM1-BCC charges) for ligand parameterization, then merges topologies.
• Explicit Solvation and Ion Addition: Solvates with selectable water models and neutralizes/adds counterions to reach a target NaCl ionic strength, recording all provenance for reproducibility.
• Use Case: When you already have a protonated receptor PDB and a docked/validated ligand SDF pose, use this to generate a simulation-ready box for running MD or downstream refinement workflows.

Quick Start

Use the drugmd-agent environment to run the build script with your receptor PDB, ligand SDF, chosen force fields, solvation settings, and an output directory.