Usage: mlmm dft [OPTIONS]
Single-point ML-region DFT with ML(dft)/MM energy recombination.
Options:
--help-advanced Show all options (including advanced settings)
and exit.
-i, --input FILE Full enzyme structure (PDB or XYZ). If XYZ,
use --ref-pdb for topology. [required]
--ref-pdb FILE Reference PDB topology when input is XYZ. XYZ
coordinates are used (higher precision) while
PDB provides atom ordering and residue
information.
--parm FILE Amber parm7 topology for the full system.
[required]
--model-pdb FILE PDB defining the ML region (atom IDs must
match the enzyme PDB). Optional when --detect-
layer is enabled.
--model-indices TEXT Comma-separated atom indices for the ML region
(ranges allowed like 1-5). Used when --model-
pdb is omitted.
--model-indices-one-based / --model-indices-zero-based
Interpret --model-indices as 1-based (default)
or 0-based. [default: model-indices-one-
based]
--detect-layer / --no-detect-layer
Detect ML/MM layers from input PDB B-factors
(B=0/10/20). If disabled, you must provide
--model-pdb or --model-indices. [default:
detect-layer]
-q, --charge INTEGER Charge of the ML region. [required]
-m, --multiplicity INTEGER Spin multiplicity (2S+1) for the ML region.
[default: 1]
--freeze-atoms TEXT Comma-separated 1-based indices to freeze
(e.g., '1,3,5').
--func-basis TEXT Exchange-correlation functional and basis set
as "FUNC/BASIS". [default:
wb97m-v/def2-tzvpd]
--max-cycle INTEGER Maximum SCF iterations. [default: 100]
--conv-tol FLOAT SCF convergence tolerance (Hartree).
[default: 1e-09]
--grid-level INTEGER DFT integration grid level (0=coarse,
3=default, 9=ultrafine). [default: 3]
-o, --out-dir DIRECTORY Output directory. [default: result_dft]
--config FILE Base YAML configuration file applied before
explicit CLI options.
--show-config / --no-show-config
Print resolved configuration and continue
execution. [default: no-show-config]
--dry-run / --no-dry-run Validate options and print the execution plan
without running DFT. [default: no-dry-run]
--convert-files / --no-convert-files
Toggle XYZ/TRJ to PDB companions when a PDB
template is available. [default: convert-
files]
-b, --backend [uma|orb|mace|aimnet2]
ML backend for the ONIOM high-level region
(default: uma).
--embedcharge / --no-embedcharge
Enable electrostatic embedding: MM point
charges are added to the PySCF QM Hamiltonian
via pyscf.qmmm.mm_charge(). [default: no-
embedcharge]
--embedcharge-cutoff FLOAT Distance cutoff (Å) from ML region for MM
point charges in xTB embedding. Default: 12.0
Å when --embedcharge is enabled.
-h, --help Show this message and exit.