drug-complex-system-builder

To build a solvated protein-ligand complex for OpenMM molecular dynamics, you need a prepared receptor PDB and a validated ligand SDF. The system applies Amber ff14SB and OpenFF Sage force fields, solvates the structure, neutralizes charges, and outputs a ready-to-run system.xml.

OpenMM MD setup uses Amber ff14SB for the protein and OpenFF Sage for ligand parameterization. Alternatively, GAFF with AM1-BCC charges can be applied to ensure accurate molecular dynamics simulation parameters.

Yes, you need a protonated receptor PDB and a docked ligand SDF pose before generating an OpenMM system bundle. Providing prepared structures allows the tool to correctly assign force fields, solvate the complex, and build the simulation box.

Yes, you can select your preferred water model and target NaCl ionic strength when solvating a protein-ligand complex. The process adds explicit solvent and counterions to neutralize charges, recording all provenance in a build_provenance.json file.

OpenMM handles ligand parameterization with OpenFF Toolkit by applying AM1-BCC charges to the ligand SDF. This process generates the necessary parameters which are then merged with the protein topology to create a unified molecular dynamics system.

Building solvated protein-ligand systems supports simulation box construction for cube or common truncated shapes. This ensures the generated OpenMM molecular dynamics system fits standard periodic boundary conditions for accurate dynamics calculations.