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.