oniom-export

Overview

Summary: Export an Amber-topology ML/MM system into external QM/MM input formats (Gaussian ONIOM or ORCA QM/MM).

Unified Command

mlmm oniom-export --parm real.parm7 -i pocket.pdb --model-pdb ml.pdb \
 -o out.<gjf|com|inp> --mode <g16|orca> -q 0 -m 1

• --mode is highest priority.

• If --mode is omitted, mode is inferred from -o:

  • .gjf/.com -> g16

  • .inp -> orca

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

Quick chooser

If you need…	Use
Gaussian ONIOM input with link-atom annotations	mlmm oniom-export --mode g16
ORCA QM/MM input with ORCAFF handling	mlmm oniom-export --mode orca

See Also

• Common Error Recipes – Symptom-first failure routing

• Troubleshooting – Detailed troubleshooting guide

• oniom_gaussian – Gaussian-mode details (--mode g16)

• oniom_orca – ORCA-mode details (--mode orca)

• oniom_import – Reconstruct XYZ/layered PDB from ONIOM inputs

• mm_parm – Build Amber topology

• define_layer – Build/check layer annotations