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