The first non-commentary line of a
.mmol file is the number of atoms
in the molecule. After it the corresponding number of lines follows, one
line per atom. Each line contains 8 compulsory
parameters. They are: 1) atom name in the program; 2),3) and 4) are the
initial X,Y,Z coordinates of the atom in the molecular coordinate system,
5) mass in atom units, 6) charge, 7) Lennard-Jones parameter
(effective atom diameter) in Å, 8) Lennard-Jones parameter
in kJ/M. Two optional columns may present, the 9-th column with the
chemical types of atoms according to the chosen force field and the 10th,
with the atom numbers.
This part is concluded by a reference to the molecular structure/ force field which is read by the program and printed in the output. It consists of the first line with a number specifying the number of lines for the reference, followed by the corresponding number of lines with the reference itself.