oniom-export

Export an Amber-topology ML/MM system into an external QM/MM input file — Gaussian ONIOM (--mode g16, with link-atom annotations) or ORCA QM/MM (--mode orca, with ORCAFF handling). It combines an Amber parm7 topology, a coordinate file, and the ML-region (QM) definition into a single ready-to-run input file: the QM region is taken from --model-pdb, and the surrounding MM environment is emitted in the target program’s native format with link-atom annotations at the QM/MM cut.

Examples

# Gaussian ONIOM input
mlmm oniom-export --parm real.parm7 -i pocket.pdb --model-pdb ml.pdb \
 -o out.gjf --mode g16 -q 0 -m 1

# ORCA QM/MM input (mode inferred from the .inp suffix)
mlmm oniom-export --parm real.parm7 -i pocket.pdb --model-pdb ml.pdb \
 -o out.inp -q 0 -m 1

# Gaussian input with a custom method/basis and resources
mlmm oniom-export --parm real.parm7 -i pocket.pdb --model-pdb ml.pdb \
 -o out.gjf --mode g16 --method 'wb97xd/def2-svp' --nproc 16 --mem 32GB -q 0 -m 1

Workflow

  1. Topology + coordinates — read the parm7 and the -i coordinate file (atom order must match the topology; --element-check validates the element sequence).

  2. QM region — --model-pdb defines the QM (ML-region) atoms; --near sets the movable/active MM cutoff (Å).

  3. Link atoms — placed at each severed QM/MM bond. --link-atom-method scaled (default) uses the Morokuma/Dapprich g-factor (matches the MLMMCore runtime); fixed uses fixed 1.09/1.01 Å bond lengths.

  4. Write — emit the target-format input file at -o. ORCA mode additionally resolves ORCAFF.prms (auto-converting from Amber via orca_mm -convff -AMBER when --convert-orcaff is on).

Outputs

  • <output>.{gjf,com} (g16) or <output>.inp (ORCA) — the QM/MM input file

  • ORCA mode also reads/creates <parm7_stem>.ORCAFF.prms in the output directory (force-field parameters)

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) for the current structure.

None

--model-pdb PATH

PDB defining the QM-region atoms.

None

-o, --output PATH

Output file path (.gjf / .com for g16, .inp for ORCA).

Required

--mode [g16|orca]

Export mode; inferred from the -o suffix when omitted.

inferred

--method TEXT

QM method and basis set.

mode-dependent

-q, --charge INT

Charge of the QM region.

Required

-m, --multiplicity INT

Multiplicity of the QM region.

1

--near FLOAT

Distance cutoff (Å) for movable/active MM atoms.

6.0

--nproc INT

Number of processors.

8

--mem TEXT

Memory allocation (g16 mode).

16GB

--total-charge INT / --total-mult INT

Total charge / multiplicity of the full QM+MM system (ORCA Charge_Total / Mult_Total).

None

--orcaff PATH

Path to ORCAFF.prms (ORCA mode); created in the output directory if omitted.

None

--convert-orcaff / --no-convert-orcaff

Auto-convert a missing ORCAFF.prms via orca_mm -convff -AMBER (ORCA mode).

True

--element-check / --no-element-check

Validate the --input element sequence against the parm7 topology.

True

--link-atom-method [scaled|fixed]

Link-H placement: scaled (g-factor, matches runtime) or fixed (1.09/1.01 Å).

scaled

mlmm oniom-export --help shows core options; mlmm oniom-export --help-advanced shows the full list.

Notes

  • Mode selection: --mode is highest priority. If --mode is omitted, the mode is inferred from -o:

    • .gjf / .com → g16

    • .inp → orca

  • If --mode is omitted and the -o suffix is unknown, the command fails.

See Also