Next: The force field (.ff) Up: Makemol utility Previous: Makemol utility

## General organization

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.

Next: The force field (.ff) Up: Makemol utility Previous: Makemol utility