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## The molecular structure (.smol) file

This file contains information on molecular structure, partial atomic charges and the force field atom types. All the lines beginning with ``#'' are considered as commentaries. The first non-commentary line defines the number of atoms in the molecule. Then follows the corresponding number of lines describing each atom. Each line consists of 6 parameters. The first one is the name of the atom. Parameters 2 - 4 are the initial X, Y and Z coordinates of atoms. The 5-th parameter is the partial atom charge, and the 6th parameter is the force field atom type. `Makemol` just rewrites parameters 1-5 into corresponding sections of the `.mmol` file, and uses the force field atom type (6th parameter) in order to find the force field parameters from the `.ff` file.

`Makemol` defines masses of atoms from the one or two first letters in the atom name (the first column of `.smol` file). If the program cannot recognize the element, it complains about that; in such a case the mass of the atom must be put manually into resulting `.mmol` file.

After the description of atoms, a section describing the bond structure follows. The first line of this section is the number of bonds. Then the corresponding number of lines follows, with two numbers in each line defining numbers of atoms bound by the corresponding bond. From this list, `Makemol` builds lists of covalent angles and torsions angles, and substitute the corresponding force field parameters.

Besides the described above `.smol` format, `Makemol` can accept `alchemy` and CHARMM-coordinate formats which contain similar information in the corresponding fields.

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