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Molecular geometry and non-bonded interaction parameters

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 $\sigma$ (effective atom diameter) in Å, 8) Lennard-Jones parameter $\epsilon$ 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.

Alexander Lyubartsev 2010-01-07