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## Bonds

Two types of bonds are implemented, standard harmonic bond (Note: no factor 1/2 in the potential):

| (4)

and Morse potential:

| (5)

Harmonic bonds may be also used for description of the so-called Urey-Bradley term which is a harmonic potential between the 1-3 neighbors (atoms separated by two covalent bonds). This term is included for example into CHARMM force field as a part of interaction potential for covalent angles.

The first line of the bond section of a `.mmol` file is the number of bonds. Then lines, one per each bond, follow with parameters for each bond. Each line consists of the following fields:

- The first is the type of the bond potential. Available values are 0 (harmonic bond), 1 (Morse potential) and 2 (Urey-Bradley term). In the case of the Urey-Bradley term, the interaction is calculated exactly as in the case of a harmonic bond (type 0), but the corresponding bond is not accounted for definition of 1-3 and 1-4 neighbors.

- The second and third parameters are atom numbers which are linked by the bond.

- The fourth field is the equilibrium bond length in Å

- The 5-th parameter is the force constant in

- The 6-th and 7-th parameters are used only for the Morse-type bonds and define the () and () parameters of the Morse potential respectively

Next: Covalent angles Up: Description of the molecular Previous: Molecular geometry and non-bonded