.mcm

Coarse-grain topology file, which is similar to CG.mmol, but includes information about bead/CG-atom types and intramolecular bonds. In general it consists of three parts: the first part describes atoms involved in the molecule, the second part contains list of covalent-like bonds and the third part lists angle-bending bonds. An individual .mcm file should be provided for each molecular type present in the system. These files are automatically generated by rdf.py utility during computation of th e reference distribution functions.

Format of .mcm file:
NB! Lines beginning with '#' or '!' are commentaries, they are dropped while parsing the file.
First the atom description block is specified:
1 line: Number of bead/atoms in the molecule (Natoms)
Natoms lines: Atom records. One record per line.
Each record contains 8 parameters. Atom name; X,Y,Z coordinates (Å) of the atom in a local coordinate system, mass (au.); charge (el.); index of the atom type; name of bead/atom type. The short-range non-bonded interaction between a pair of beads/atoms will be defined by the bead/atom types defined in this file. Atoms of the same atom type interact by the same non-bonded potential.
Then the pairwise bond block is specified:
1 line: The total number of pairwise bond types present in the molecule (Nbonds).
Then for every individual bond type (of Nbonds) one need to specify:
1 line: Number of atom pairs which are involved in the bond of this type (NPairs);
NPairs lines: List of such atom pairs, one pair per line.
Then the angle bending bond block is specified:
1 line: Total number of angle bending bond types present in the molecule. For every individual bond type (NAngles) one need to specify:
1 line: Number of atom triplets which are involved in the bond of this type (NAngles);
NAngles lines: List of such atom triplets, one triplet per line.

NB! In the first version of MagiC the triplet used to had unusual order: central atom stands last in the triple, e.g. triplet 1 3 2, defines angle between 1-2 and 2-3. Now it is changed to the regular 1-2-3 order, and to avoid misunderstanding rdf.py utility automatically writes Order=1-2-3 after the number of total angle bending bonds.