Usage: mlmm opt [OPTIONS]
ML/MM geometry optimization with LBFGS (light) or RFO (heavy).
Options:
--help-advanced Show all options (including advanced settings)
and exit.
-i, --input FILE Input structure file (PDB, XYZ). XYZ provides
higher coordinate precision. If XYZ, use
--ref-pdb to specify PDB topology for atom
ordering and output conversion. [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 for output conversion.
--parm FILE Amber parm7 topology covering the whole enzyme
complex. [required]
--model-pdb FILE PDB defining atoms that belong to the ML
(high-level) region. 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 ML region charge. Required unless --ligand-
charge is provided.
-l, --ligand-charge TEXT Total charge or per-resname mapping (e.g.,
GPP:-3,SAM:1) used to derive charge when -q is
omitted (requires PDB input or --ref-pdb).
-m, --multiplicity INTEGER Spin multiplicity (2S+1) for the ML region.
Defaults to 1 when omitted.
--freeze-atoms TEXT Comma-separated 1-based atom indices to freeze
(e.g., '1,3,5').
--radius-partial-hessian, --hess-cutoff FLOAT
Distance cutoff (Å) from ML region for MM
atoms to include in Hessian calculation.
Applied to movable MM atoms and can be
combined with --detect-layer. `--hess-cutoff`
is a compatibility alias.
--radius-freeze, --movable-cutoff FLOAT
Distance cutoff (Å) from ML region for movable
MM atoms. MM atoms beyond this are frozen.
Providing --radius-freeze disables --detect-
layer and uses distance-based layer
assignment. `--movable-cutoff` is a
compatibility alias.
--dist-freeze TEXT Distance restraints: inline Python literal
(e.g. '[(1,5,1.4)]') or a YAML/JSON spec file
path. Same format as --scan-lists:
(i,j,target_A) triples. Target may be omitted
to freeze at the current distance: (i,j).
--one-based / --zero-based Interpret --dist-freeze / --scan-lists indices
as 1-based (default) or 0-based. [default:
one-based]
--bias-k FLOAT Harmonic restraint strength k [eV/Å^2] for
--dist-freeze. [default: 300.0]
--max-cycles INTEGER Maximum number of optimization cycles.
[default: 10000]
--dump / --no-dump Write optimization trajectories
('optimization_trj.xyz' and
'optimization_all_trj.xyz'). [default: no-
dump]
-o, --out-dir TEXT Output directory. [default: ./result_opt/]
--thresh [gau_loose|gau|gau_tight|gau_vtight|baker|never]
Convergence preset.
--opt-mode [grad|hess|light|heavy|lbfgs|rfo]
Optimization mode: grad (lbfgs) or hess (rfo).
Aliases light/heavy and lbfgs/rfo are
accepted. [default: grad]
--microiter / --no-microiter Enable microiteration: alternate ML 1-step
(RFO) and MM relaxation (LBFGS with MM-only
forces). Only effective in --opt-mode hess
(RFO). Ignored in grad mode. [default:
microiter]
--flatten / --no-flatten Enable/disable imaginary-mode flatten loop
after optimization. [default: no-flatten]
--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 optimization. [default: no-
dry-run]
--convert-files / --no-convert-files
Convert XYZ/TRJ outputs into PDB companions
based on the input format. [default: convert-
files]
-b, --backend [uma|orb|mace|aimnet2]
ML backend for the ONIOM high-level region
(default: uma).
--embedcharge / --no-embedcharge
Enable xTB point-charge embedding correction
for MM→ML environmental effects. [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.