The makemol utility is used to generate a .mmol file
(containing information on both molecular structure and the force field)
from two files: a force field (.ff) file, with information about
force field parameters, and a .smol file, which contains only
structural information about the molecule (initial atom coordinates,
the list of covalent bonds, the partial atomic charges, and the chemical
types of atoms (which should match the types in the force field file).
The utility constructs the list of covalent angles and torsion angles,
and pick up the force field parameters from the force field file. If some
parameters are not found in the force field file, the corresponding line
in the resulting .mmol file is marked with an exclamation mark,
and a note is written on the screen and in the makefile.log file.
The list of Improper torsions is not generated automatically. If impropers
exist for the given molecule, they should be added into .mmol file
manually.
The utility is run in a self-explaining dialog regime. The format of the force field and the molecular structure files is explained below.