ORCA QM/MM Mode (oniom-export --mode orca)

Overview

Summary: Export an ML/MM system to ORCA QM/MM (.inp) using an Amber parm7 topology.

Minimal example

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

Output checklist

  • system.inp

  • ORCAFF.prms (either reused, provided, or auto-generated)

Common examples

  1. Basic export.

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

  1. Set explicit total charge/multiplicity for full QM+MM system.

mlmm oniom-export --mode orca --parm real.parm7 -i pocket.pdb --model-pdb ml_region.pdb \
 -o system.inp -q 0 -m 1 --total-charge -1 --total-mult 1

  1. Use an explicit ORCAFF path and disable auto conversion.

mlmm oniom-export --mode orca --parm real.parm7 -i pocket.pdb --model-pdb ml_region.pdb \
 -o system.inp --orcaff ./ORCAFF.prms --no-convert-orcaff

Workflow

ORCA mode (mlmm oniom-export --mode orca) reads topology information from --parm and writes ORCA QM/MM input.

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

  2. Optionally load coordinates and validate element ordering (--element-check).

  3. Map --model-pdb atoms to the full system to define QM atoms.

  4. Resolve ORCAFF parameters from --orcaff or auto-generated default.

  5. Write ORCA .inp with method, parallel settings, QM set, and total charge/multiplicity fields.

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 ORCA input file (.inp).

Required

--method TEXT

QM method and basis set.

B3LYP D3BJ def2-SVP

-q, --charge INT

Charge of QM region.

Required

-m, --multiplicity INT

Multiplicity of QM region.

1

--total-charge INT

Total charge of full QM+MM system (Charge_Total).

topology-derived

--total-mult INT

Total multiplicity of full QM+MM system (Mult_Total).

same as --multiplicity

--nproc INT

Number of processors.

8

--near FLOAT

Distance cutoff (Å) used to define ActiveAtoms when layer tags are absent.

6.0

--orcaff PATH

Path to ORCAFF.prms.

None (auto-resolved to <parm7_stem>.ORCAFF.prms)

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

Attempt orca_mm -convff -AMBER when ORCAFF is missing.

True

See Also