Usage: nanobabel [action] [options]
all actions:
minimize Molecular energy minimization
bonding Compute bonding information of molecule
convert Rewrite molecule file in a different format
hydrogen Add or remove hydrogens from a molecule file
forcefields List supported forcefields
formats List supported file formats
descriptors List supported descriptors
plugins List supported plugins
config Current configuration informations
minimize options:
-i FILE Input file (default=input.pdb)
-o FILE Output file (default=output.pdb)
-cx FILE Forcefield constraints file
-ff FFID Select a forcefield (default=UFF)
-h Add hydrogen atoms
-n steps Specify the maximum number of steps (default=2500)
-l steps Specify the interval number of steps between structure updates
-dd PATH Set the path for the data directory
bonding options:
-i FILE Input file (default=input.pdb)
-o FILE Output file (default=output.pdb)
-h Add hydrogen atoms
-dd PATH Set the path for the data directory
convert options:
-i FILE Input file (default=input.pdb)
-o FILE Output file (default=output.pdb)
-h Add hydrogen atoms
-dd PATH Set the path for the data directory
hydrogen options:
-i FILE Input file (default=input.pdb)
-o FILE Output file (default=output.pdb)
-add Add hydrogen atoms
-del Delete hydrogen atoms
-dd PATH Set the path for the data directory