.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 the reference distribution functions, but they can be manually edited if necessary. For example, partial charges of the CG sites can be corrected.

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 the 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.