Usage: mlmm scan [OPTIONS]
Bond-length driven scan with staged harmonic restraints and relaxation
(ML/MM).
Options:
--help-advanced Show all options (including advanced settings)
and exit.
-i, --input FILE Full-enzyme PDB used by the ML/MM calculator
and as reference for conversions. [required]
--parm FILE Amber parm7 topology covering the entire
enzyme complex. [required]
--model-pdb FILE PDB defining the ML-region atoms for ML/MM.
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
(ML=0, MovableMM=10, FrozenMM=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').
--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.
--movable-cutoff FLOAT Distance cutoff (Å) from ML region for movable
MM atoms. MM atoms beyond this are frozen.
Providing --movable-cutoff disables --detect-
layer.
-s, --scan-lists TEXT Scan targets: inline Python literal (e.g.
'[(1,5,1.4)]') or a YAML/JSON spec file path.
Multiple inline literals define sequential
stages.
--one-based / --zero-based Interpret (i,j) indices in --scan-lists as
1-based (default) or 0-based. [default: one-
based]
--print-parsed / --no-print-parsed
Print parsed scan targets after resolving
-s/--scan-lists. [default: no-print-parsed]
--max-step-size FLOAT Maximum change in any scanned bond length per
step [Å]. [default: 0.2]
--bias-k FLOAT Harmonic well strength k [eV/Å^2]. [default:
300]
--opt-mode [grad|hess|lbfgs|rfo|light|heavy]
Compatibility option for mlmm all forwarding.
Scan relaxations always use LBFGS; values
other than grad/lbfgs/light emit a warning.
--max-cycles INTEGER Maximum LBFGS cycles per biased step and per
(pre|end)opt stage. [default: 10000]
--relax-max-cycles INTEGER Compatibility alias of --max-cycles (overrides
it when provided).
--dump / --no-dump Write per-step optimizer trajectory files.
scan_trj.xyz and scan.pdb are always written
per-stage and as a combined file in out-dir,
regardless of this flag. [default: no-dump]
-o, --out-dir TEXT Base output directory. [default:
./result_scan/]
--thresh [gau_loose|gau|gau_tight|gau_vtight|baker|never]
Convergence preset for relaxations.
--config FILE Base YAML configuration file applied before
explicit CLI options.
--ref-pdb FILE Reference PDB topology to use when --input is
XYZ (keeps XYZ coordinates).
--preopt / --no-preopt Pre-optimize initial structure without bias
before the scan. [default: no-preopt]
--endopt / --no-endopt After each stage, run an additional unbiased
optimization of the stage result. [default:
no-endopt]
--dry-run / --no-dry-run Validate options and print the execution plan
without running the scan. [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. Only used when --embedcharge is enabled.
--link-atom-method [scaled|fixed]
Link-atom position mode: scaled (g-factor,
default) or fixed (legacy 1.09/1.01 Å).
--mm-backend [hessian_ff|openmm]
MM backend: hessian_ff (analytical Hessian,
default) or openmm (finite-difference Hessian,
slower).
--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]
-h, --help Show this message and exit.