The energy is again calculated. The structure is then said to be optimized. It is frequently necessary to optimize several different conformations to get a realistic idea of which is the lowest energy conformation of the molecule. DTMM includes a very unusual feature in its calculations where it treats a group of atoms as a fragment so that it can rotate the fragment in an effort to locate local minima. Most programs require a systematic rotation of the various torsion angles involved to achieve this.
Molecular mechanics requires lots of known values to be recognised.
These are put into the program as parameters. These values include equilibrium bond lengths, equilibrium bond angles, force constants, and torsion angle degeneracies for rotatable bonds. For parameters to be correlated to the molecule each atom must have a type. Most programs require you to specify this or allow you the option of changing atom types. DTMM assumes type from the atom name and connectivity.