mmml make-res¶
CGENFF residue → PDB/PSF/topology.
Usage¶
mmml make-res --help
Options¶
usage: mmml make-res [-h] [--res RES] [--list-residues] [--no-pager]
[--skip-energy-show]
Generate a CGENFF residue (PDB, PSF, topology) via PyCHARMM.
Input & configuration:
--list-residues List valid CGENFF residue names and descriptions (opens
less on a TTY).
Scientific model:
--skip-energy-show Skip the final CHARMM energy.show() (avoids segfault on
some clusters/SLURM).
Diagnostics & safety:
-h, --help show this help message and exit
Other options:
--res RES CGENFF residue name (RESI in top_all36_cgenff.rtf), e.g.
ACO, CYBZ, TIP3.
--no-pager With --list-residues, print the table to stdout instead of
piping to less.
Examples: mmml make-res --list-residues mmml make-res --list-residues --no-pager
| grep -i acetone mmml make-res --res ACO
Example structures¶
More detail: Structure building guide.