Usage: mlmm tsopt [OPTIONS]
TS optimization: grad (Dimer) or hess (RS-I-RFO) for the ML/MM calculator.
Options:
--help-advanced Show all options (including advanced settings)
and exit.
-i, --input FILE Starting geometry (PDB or 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 for the whole enzyme (MM
region). [required]
--model-pdb FILE PDB containing the ML-region atoms. 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 Total charge of the ML region. 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.
--freeze-atoms TEXT Comma-separated 1-based indices to freeze
(e.g., '1,3,5').
--radius-hessian, --hess-cutoff FLOAT
Distance cutoff (Å) from ML region for MM
atoms to include in Hessian calculation.
Applied to movable MM atoms. Default 0.0 means
ML-only partial Hessian. [default: 0.0]
--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.
--hessian-calc-mode [analytical|finitedifference]
How the ML backend builds the Hessian
(Analytical or FiniteDifference); overrides
calc.hessian_calc_mode from YAML. Default:
'FiniteDifference'. Use 'Analytical' when VRAM
is sufficient.
--max-cycles INTEGER Maximum total optimization cycles. [default:
10000]
--dump / --no-dump Write concatenated trajectory
'optimization_all_trj.xyz'. [default: no-
dump]
-o, --out-dir TEXT Output directory. [default: ./result_tsopt/]
--thresh [gau_loose|gau|gau_tight|gau_vtight|baker|never]
Convergence preset.
--opt-mode [grad|hess|light|heavy|dimer|rsirfo]
grad (dimer) or hess (rsirfo). Aliases
light/heavy and dimer/rsirfo are accepted.
[default: hess]
--microiter / --no-microiter Enable microiteration: alternate ML 1-step
(RS-I-RFO) and MM relaxation (LBFGS with MM-
only forces). Only effective in --opt-mode
hess. Ignored in grad mode. [default:
microiter]
--partial-hessian-flatten / --full-hessian-flatten
Use partial Hessian (ML region only) for
imaginary mode detection in flatten loop.
[default: partial-hessian-flatten]
--flatten / --no-flatten Enable/disable extra imaginary-mode flattening
loop. --flatten uses the default
flatten_max_iter (50); --no-flatten forces it
to 0. When not provided, the value is
determined by the YAML config or defaults.
--ml-only-hessian-dimer / --no-ml-only-hessian-dimer
Use ML-region-only Hessian (no MM Hessian
contribution) for dimer orientation in grad
mode. Faster but less accurate for mode
direction. [default: no-ml-only-hessian-
dimer]
--active-dof-mode [all|ml-only|partial|unfrozen]
Active DOF selection for final frequency
analysis: all (all atoms), ml-only (ML only),
partial (ML + MovableMM, default), unfrozen
(all except frozen layer). [default: partial]
--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 TS 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.