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

Export an ML/MM system to Gaussian ONIOM (.com/.gjf) using an Amber parm7 topology. This is the Gaussian-specific detail page for oniom-export; it reads topology data from --parm (via ParmEd) and optional coordinates from -i/--input, then writes a Gaussian ONIOM input file with method, layer flags, and connectivity.

Examples

Minimal export with explicit charge and multiplicity:

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

# 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

# Set compute resources and the movable-atom cutoff
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

  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, %nprocshared, %mem, coordinates, layer flags, and connectivity.

Outputs

  • system.com or system.gjf

  • Console summary of detected QM atoms and boundary handling

CLI options

The full flag list is in the generated command reference; the table below covers the options that need explanation.

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 MM atoms.

6.0

--nproc INT

Number of processors.

8

--mem TEXT

Memory allocation.

16GB

See Also