oniom-orca

Export an ML/MM system to ORCA QM/MM (.inp) using an Amber parm7 topology. This is the ORCA-specific detail page for oniom-export (mlmm oniom-export --mode orca). It reads topology information from an Amber parm7 file, maps a model-region PDB to the QM atoms, resolves ORCAFF parameters, and writes an ORCA QM/MM input. The input is runnable only when the referenced ORCAFF parameter file exists.

The input parm7 must be CMAP-free. ORCA’s MM engine does not apply CMAP terms, so export fails before writing when the topology contains them.

Examples

Basic export:

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

Set explicit total charge/multiplicity for the full QM+MM system:

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

Use an explicit ORCAFF path and disable auto-conversion:

mlmm oniom-export --mode orca --parm real.parm7 -i pocket_layered.pdb --model-pdb ml_region.pdb \
 -o system.inp -q 0 -m 1 --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. Load coordinates and the movable/frozen layers from the input PDB B-factors, then 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.

Outputs

  • system.inp

  • ORCAFF.prms when provided, reused, or successfully generated. If conversion is unavailable, the command reports the missing parameter file; the .inp is incomplete until that file is supplied.

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 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

--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