Usage: mlmm define-layer [OPTIONS]
Define 3-layer ML/MM system based on distance from ML region.
Options:
--help-advanced Show all options (including advanced settings)
and exit.
-i, --input FILE Input PDB file containing the full system.
[required]
--model-pdb FILE PDB file defining atoms in the ML region.
--model-indices TEXT Comma-separated atom indices for ML region
(e.g., '0,1,2,3' or '1-10,15,20-25'). Takes
precedence over --model-pdb.
--radius-partial-hessian FLOAT Deprecated in 3-layer mode (ignored).
[default: 0.0]
--radius-freeze FLOAT Distance cutoff (Å) from ML region for movable
MM atoms. Atoms beyond this distance are
frozen. [default: 8.0]
-o, --output FILE Output PDB file with B-factors set to layer
values. Defaults to '<input>_layered.pdb'.
--one-based / --zero-based Interpret --model-indices as 1-based (default)
or 0-based. [default: one-based]
-h, --help Show this message and exit.