mmml make-box¶
Pack molecules into a periodic box.
Usage¶
mmml make-box --help
Options¶
usage: mmml make-box [-h] [--n N] [--res RES] [--side_length SIDE_LENGTH]
[--pdb PDB] [--solvent SOLVENT] [--density DENSITY]
Pack a solute into a periodic box (vacuum copies or explicit solvent). Stages
--pdb to pdb/initial.pdb when given, then runs Packmol + CHARMM.
Input & configuration:
--pdb PDB Solute PDB (CGenFF residue/atom names). Copied to
pdb/initial.pdb before Packmol. When omitted,
pdb/initial.pdb must already exist (e.g. from mmml make-
res).
Scientific model:
--density DENSITY Solvent (or neat liquid) density in kg/m³. Built-in for
TIP3/water (1000) and OCOH/octanol (824); required for
other solvents when sizing N from density.
Diagnostics & safety:
-h, --help show this help message and exit
Other options:
--n N
--res RES Tag for output files (psf/system-<res>.psf,
pdb/init-<res>.pdb).
--side_length, --box-size SIDE_LENGTH
Cubic box side length in Å. '--box-size' is an alias,
matching the naming used elsewhere in the CLI suite.
--solvent SOLVENT CGenFF solvent residue name (any RESI in
top_all36_cgenff.rtf), e.g. TIP3, MEOH, ACO, OCOH, ACN,
DMSO. Aliases: water→TIP3, octanol→OCOH.
Example structures¶
More detail: Structure building guide.