Gaussian ONIOM Mode (oniom-export --mode g16)

Overview

Summary: Export an ML/MM system to Gaussian ONIOM (.com/.gjf) using an Amber parm7 topology.

Minimal example

mlmm oniom-export --mode g16 --parm real.parm7 -i pocket.pdb --model-pdb ml_region.pdb \
 -o system.com -q 0 -m 1

Output checklist

• system.com or system.gjf

• Console summary of detected QM atoms and boundary handling

Common examples

1. Basic export with explicit method.

mlmm oniom-export --mode g16 --parm real.parm7 -i pocket.pdb --model-pdb ml_region.pdb \
 -o system.com --method "wB97XD/def2-TZVPD"

2. Disable element-sequence validation when atom order is already trusted.

mlmm oniom-export --mode g16 --parm real.parm7 -i pocket.xyz --model-pdb ml_region.pdb \
 -o system.gjf --no-element-check

3. Tune optimization environment metadata.

mlmm oniom-export --mode g16 --parm real.parm7 -i pocket.pdb --model-pdb ml_region.pdb \
 -o system.com --nproc 16 --mem 32GB --near 5.0

Workflow

Gaussian mode (mlmm oniom-export --mode g16) reads topology data from --parm (via ParmEd), optional coordinates from -i/--input, then writes a Gaussian ONIOM input file.

1. Load atom/bond/charge data from parm7.

2. Optionally load coordinates and run element-order validation (--element-check).

3. If --model-pdb is provided, map those atoms to define the QM layer.

4. Detect QM/MM boundaries and annotate link atoms.

5. Write Gaussian input with method, %nproc, %mem, coordinates, layer flags, and connectivity.

CLI options

Option	Description	Default
--parm PATH	Amber parm7 topology file.	Required
-i, --input PATH	Coordinate file (PDB/XYZ); atom order must match parm7.	None
--element-check / --no-element-check	Validate element sequence between input and parm7.	True
--model-pdb PATH	PDB file defining QM region atoms.	None
-o, --output PATH	Output Gaussian input file (.com or .gjf).	Required
--method TEXT	QM method and basis set.	wB97XD/def2-TZVPD
-q, --charge INT	Charge of QM region.	Required
-m, --multiplicity INT	Multiplicity of QM region.	1
--near FLOAT	Distance cutoff (Å) for movable atoms.	6.0
--nproc INT	Number of processors.	8
--mem TEXT	Memory allocation.	16GB

See Also

• oniom_orca – ORCA mode guide (--mode orca)

• oniom_export – Export overview and chooser

• mm_parm – Build Amber topology (parm7/rst7)

• define_layer – Build/check layer annotations

• Common Error Recipes – Symptom-first failure routing

• Troubleshooting – Detailed troubleshooting guide