OpenFF Ligand PArametrization

for Gromacs

Reads an SDF file, parametrizes each molecule with the OpenFF force field, and writes one folder per ligand containing Gromacs-ready files.

Usage

1. Create environment and install dependencies

macOS / Linux

bash setup_env.sh

Windows

setup_env.bat

2. Activate the environment

conda activate openff_env

3. Run parametrization

python parametrize.py run example.sdf --outdir output

4. Verify output files (optional)

python parametrize.py verify example.sdf --outdir output

Output structure

output/
	CHEMBL45305/
		ligand.gro      # coordinates (Gromacs format)
		ligand.pdb      # coordinates (PDB format)
		topol.top       # force field topology

Notes

Coordinates

Coordinates are read from the SDF via RDKit (removeHs=False). No minimization or conformation generation is performed. Input molecules are registered as 2D in the SDF header, but contain valid 3D coordinates.

Warnings

The following warnings may appear during execution and can be safely ignored:

RDKit 2D/3D warning

Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero.

Input molecules are flagged as 2D in the SDF header despite having 3D geometry.

PyTorch FutureWarning

FutureWarning: torch.distributed.reduce_op is deprecated

Caused by an internal PyTorch compatibility issue inside openff-interchange. Not related to this pipeline.

To suppress all warnings, keep suppress_warnings() enabled in main(). To show warnings, comment out that line.

Requirements

See environment.yml (conda) or requirements.txt (pip). All dependencies are installed automatically by the setup script.