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/mmCIF, or XYZ with
--ref-pdb 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.
--parm7, --parm FILE Amber parm7 topology for the full system.
[required]
--model-pdb FILE ML-only, link-H-free PDB subset; atom
identity/order must match the full PDB/parm7.
When provided, it defines ML membership;
--detect-layer still reads valid
movable/frozen MM B-factors.
--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 (PDB inputs or XYZ with --ref-pdb) or
YAML calc.model_charge gives it.
-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/mmCIF
input or --ref-pdb).
-m, --multiplicity INTEGER RANGE
Spin multiplicity (2S+1) for the ML region;
YAML applies when omitted. [default: (1);
x>=1]
--func-basis TEXT Exchange-correlation functional and basis set
as "FUNC/BASIS". [default: wb97m-v/def2-svp]
--scf-max-cycles, --max-cycle INTEGER RANGE
Maximum SCF iterations. [default: 100; x>=1]
--scf-tol, --conv-tol FLOAT SCF energy convergence threshold (ΔE in
Hartree between SCF cycles). [default: 1e-09]
--dft-grid-level, --grid-level INTEGER
DFT integration grid level (0=coarse,
3=default, 5=fine, 9=very fine). [default: 3]
--dft-engine, --engine [gpu|cpu]
SCF backend: gpu (GPU4PySCF, raises error if
unavailable) or cpu (PySCF). [default: gpu]
--dft-low-memory, --lowmem / --no-dft-low-memory, --no-lowmem
Use gpu4pyscf rks_lowmem.RKS for closed-shell
GPU single points, including electrostatic
embedding. Open-shell or CPU runs use standard
direct-JK RKS/UKS; --no-dft-low-memory enables
density fitting. [default: dft-low-memory]
--scf-stepwise-grid / --no-scf-stepwise-grid
Converge the SCF on a coarse grid first, then
on the final grid with the same settings.
[default: scf-stepwise-grid]
--dft-nprocs INTEGER RANGE PySCF/OpenMP CPU threads; GPU count is
unaffected. [default: (auto); x>=1]
--dft-memory, --dft-mem TEXT PySCF host RAM limit (for example 64GB or
120000MB). [default: (auto)]
-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 the loaded YAML file and its top-level
keys, then continue. [default: no-show-
config]
--dry-run / --no-dry-run Validate options and inputs without running
DFT. [default: no-dry-run]
--convert-files / --no-convert-files
Also write the ML region as PDB files (PDB
input only). [default: convert-files]
--embedcharge / --no-embedcharge
Embed MM point charges directly in the PySCF
QM Hamiltonian. The DFT workflow does not use
the optional xTB correction. [default: no-
embedcharge]
--embedcharge-cutoff FLOAT Distance cutoff (Å) from ML region for MM
point charges embedded in the PySCF QM
Hamiltonian. Only used when --embedcharge is
enabled. [default: (12.0)]
--link-atom-method [scaled|fixed]
Link-atom placement: 'scaled' (g-factor,
Gaussian ONIOM standard) or 'fixed' (1.09 Å
for C, 1.01 Å for N). [default: (scaled)]
--mm-backend [hessian_ff|openmm]
MM backend for the low-level ONIOM evaluation:
'hessian_ff' or 'openmm'. [default:
(hessian_ff)]
--cmap / --no-cmap Preserve CMAP terms in both real and model MM
layers when present in parm7. [default:
(cmap)]
--out-json / --no-out-json Write machine-readable result.json to out_dir.
[default: no-out-json]
--allow-charge-mult-mismatch Skip the ML-region charge/multiplicity
electron-parity check (logs that it was
skipped). An open-shell ML region needs a
matching multiplicity; use this only for an
intentional nonstandard input such as a
covalently-cut region.
--detect-layer / --no-detect-layer
Automatically detect ML/MM layers from input
PDB B-factors (ML=0, MovableMM=10,
FrozenMM=20) when explicit ML membership is
absent. With explicit membership, retain valid
movable/frozen MM B-factor layers. [default:
detect-layer]
-h, --help Show this message and exit.
