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 and the movable/frozen partition from an MLMM layered PDB passed to -i/--input.

The input parm7 must be CMAP-free. Gaussian ONIOM cannot represent the topology’s CMAP terms faithfully, so export fails before writing when any are present.

Examples

Minimal export with explicit charge and multiplicity:

mlmm oniom-export --mode g16 --parm real.parm7 -i pocket_layered.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_layered.pdb --model-pdb ml_region.pdb \
 -o system.com -q 0 -m 1 --method "wB97XD/def2-TZVPD"

# Disable element-sequence validation when atom order is already trusted
mlmm oniom-export --mode g16 --parm real.parm7 -i pocket_layered.pdb --model-pdb ml_region.pdb \
 -o system.gjf -q 0 -m 1 --no-element-check

# Set compute resources
mlmm oniom-export --mode g16 --parm real.parm7 -i pocket_layered.pdb --model-pdb ml_region.pdb \
 -o system.com -q 0 -m 1 --nproc 16 --mem 32GB

Workflow

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

  2. Load coordinates and the movable/frozen layers from the input PDB B-factors, then 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

MLMM layered PDB; atom order must match parm7.

Required

--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

--nproc INT

Number of processors.

8

--mem TEXT

Memory allocation.

16GB

See Also