Usage: mlmm mm-parm [OPTIONS]
Generate Amber parm7/rst7 (and a LEaP-exported PDB) from a PDB using
AmberTools only.
Options:
--help-advanced Show all options (including advanced settings)
and exit.
-i, --input FILE Input PDB file (used as-is; optional hydrogens
via --add-h/--ph). [required]
--out-prefix TEXT Output prefix (default: input PDB stem). For
LEaP PDB: if omitted and --add-h True,
<input_stem>_parm.pdb is used.
-l, --ligand-charge TEXT Comma-separated mapping of residue=charge or
residue:charge (e.g., "GPP=-3,MMT=-1" or
"GPP:-3,MMT:-1")
--ligand-mult TEXT Comma-separated mapping of residue=multiplicity
or residue:multiplicity (e.g., "HEM=1,NO:2")
--keep-temp / --no-keep-temp Keep temporary working directory (in current
dir) for debugging. [default: no-keep-temp]
--add-ter / --no-add-ter Insert TER before/after target residues. When
contiguous, TER is not inserted between them.
[default: add-ter]
--add-h / --no-add-h Add hydrogens using PDBFixer at the specified
--ph. [default: no-add-h]
--ph FLOAT pH used by PDBFixer when adding hydrogens
(--add-h True). Default: 7.0
--ff-set [ff19SB|ff14SB] Force-field set for proteins/backbone typing and
water/ion parameters (default: ff19SB).
-h, --help Show this message and exit.