mlmm-toolkit Documentation

Version: v0.3.0 — Python CLI for ML/MM ONIOM analyses of enzymatic reactions.

Quick start

Goal	Page
Install + run a first end-to-end pipeline	Getting Started
3-layer ONIOM, microiteration, link atoms	Concepts & Workflow
End-to-end pipeline from a PDB	Quickstart: all
Single-structure staged scan	Quickstart: scan
TS validation (tsopt + freq)	Quickstart: tsopt
TS routes, imaginary-frequency fixes, controlled mutant comparison	tsopt
Scan modes (staged vs concerted), barrier direction	scan
Precision by GPU class	Device & HPC Setup
Symptom-first failure routing	Common Error Recipes · Troubleshooting
CLI conventions, YAML schema	CLI Conventions · YAML Reference
Python API / ML/MM calculator architecture	Python API · ML/MM Calculator
Configure GPU/CPU devices and submit on HPC	Device & HPC Setup
Terminology	Glossary

Subcommands

Subcommand	Role
all	End-to-end: ML/MM model setup → MEP → TS → IRC → freq → DFT
extract · mm-parm · define-layer · add-elem-info · fix-altloc	Structure preparation
opt · tsopt	Geometry / TS optimization
path-opt · path-search	MEP optimization / recursive refinement
scan · scan2d · scan3d	1D / 2D / 3D bond-distance scans
freq · irc	Vibrational analysis + thermochemistry / IRC (EulerPC)
dft · sp	Single-point DFT / single-point ML/MM ONIOM
bond-summary	Bond-change report between consecutive structures
trj2fig · energy-diagram	Energy plot / R→TS→P diagram
oniom-export · oniom-import	Gaussian / ORCA QM/MM round-trip

Citation

Ohmura, T., Inoue, S., Terada, T. (2025). ML/MM toolkit — Towards Accelerated Mechanistic Investigation of Enzymatic Reactions. ChemRxiv. https://doi.org/10.26434/chemrxiv-2025-jft1k

License

GNU General Public License v3 (GPL-3.0).