.mmol

MMOL is a molecular topology file format, which is inherited from MDynaMix MD software. It consists of two parts: first part describes atomic composition, geometry, charges, masses and non-bonded interactions; the second part defines bonds, angles and torsions in the molecule. MMOL-topolygy files are used by cgtraj (cgtraj) for converting high-resolution trajectory to a coarse grained one and for calculation of the reference distribution functions rdf (rdf). In both cases only information from the first section of .mmol file (information about atomic composition) is used, and the bonding part may be omitted.

The first part of the file, which is part of interest has the following structure: 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 $\sigma$ in Å, 8) Lennard-Jones parameter $\varepsilon$ in kJ/M. Two optional columns may present.

For the correct work of CGTraj utility, the only important information is the number of atoms in the molecule and masses of atoms. CGTraj utility may work without supplying .mmol files, in such case the masses of atoms are set to 1 and charges to 0.