Usage: mlmm mm-parm [OPTIONS]
Generate Amber parm7/rst7 (and a LEaP-exported PDB) from a PDB using
AmberTools; --add-h also requires PDBFixer.
Options:
-v, --verbose LEVEL Console verbosity 0-3 (default 2). 0=silent;
1=milestones only; 2=+detailed step logging
and deliverable paths; 3=everything (full
config blocks, per-file paths, DEBUG logging).
[0<=x<=3]
--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]
-o, --out-prefix TEXT Output prefix (default: input PDB stem). For
LEaP PDB: if omitted with --add-h,
<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") [default: (1)]
--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 and
disconnected peptide blocks. When target
residues are contiguous, TER is not inserted
between them. [default: add-ter]
--auto-disulfide / --no-auto-disulfide
Detect disulfides from SG-SG geometry (<= 2.5
A) across CYS/CYX and bond them, renaming a
bonded CYS to CYX so tleap drops its HG. With
--no-auto-disulfide only residues already
named CYX are bonded and CYS is left
untouched. [default: auto-disulfide]
--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). [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.