Usage: mlmm dft [OPTIONS]
Single-point ML-region DFT with ML(dft)/MM energy recombination.
Options:
-v, --verbose LEVEL Console verbosity 0-3 (default 2). 0=silent;
1=milestones only; 2=+detailed step logging
and deliverable paths; 3=everything (full
config blocks, per-file paths, DEBUG logging).
[0<=x<=3]
--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.
-q, --charge INTEGER ML region charge. Required unless --ligand-
charge is provided (PDB inputs or XYZ with
--ref-pdb).
-l, --ligand-charge TEXT Total charge or per-resname mapping (e.g.,
'SAM:1,GPP:-3') used to derive ML region
charge when -q is omitted (requires PDB input
or --ref-pdb).
-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 energy convergence threshold (ΔE in
Hartree between SCF cycles). [default: 1e-09]
--grid-level INTEGER DFT integration grid level (0=coarse,
3=default, 5=fine, 9=very fine). [default: 3]
--engine [gpu|cpu] SCF backend: gpu (GPU4PySCF, raises error if
unavailable) or cpu (PySCF). [default: gpu]
--lowmem / --no-lowmem Use gpu4pyscf rks_lowmem.RKS for closed-shell
GPU runs (memory-efficient direct JK; mlmm dft
does not call density_fit() on either path).
Open-shell or CPU engines fall back to
standard RKS/UKS automatically. [default:
lowmem]
-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]
Backend label recorded in output metadata; the
ML region in dft is computed with DFT (PySCF),
so this does not select a calculator.
--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 embedded in the PySCF QM
Hamiltonian. Default: 12.0 Å. Only used when
--embedcharge is enabled.
--link-atom-method [scaled|fixed]
Link-atom placement: 'scaled' (g-factor,
Gaussian ONIOM standard, default) or 'fixed'
(legacy 1.09 Å for C, 1.01 Å for N).
--mm-backend [hessian_ff|openmm]
MM backend for the low-level ONIOM evaluation:
'hessian_ff' (default) or 'openmm'.
--cmap / --no-cmap Enable CMAP (backbone cross-map) terms in
model parm7. Default: disabled (Gaussian
ONIOM-compatible).
--out-json / --no-out-json Write machine-readable result.json to out_dir.
[default: no-out-json]
--detect-layer / --no-detect-layer
Detect ML/MM layers from input PDB B-factors
(ML=0, MovableMM=10, FrozenMM=20). If
disabled, you must provide --model-pdb or
--model-indices. [default: detect-layer]
--model-indices-one-based / --model-indices-zero-based
Interpret --model-indices as 1-based (default)
or 0-based. [default: model-indices-one-
based]
-h, --help Show this message and exit.