What is your purpose of energy minimization? Also, minimization depends on algorithm.
Energy minimization you would like to do for finding minimum energy conformations, relieve the strain in structures obtained from experiments, or for finding a local or global energy minimum conformation.
In such cases, the potential energy function should include terms such as: bond stretching, angle bending, torsions, pairwise interactions (vdW and electrostatics), and other terms such as constraints.
Constraints are often required to be uses in order to force molecules to desired conformations, which include distances and angles to keep some of variables to their target values, and their are included as additional terms.
Forcefield topology and parameters that you should use, which are widely seen in publications, include: charmm all atom force fields, amber (see @Alexey comments), gromacs, opls.
Location of the global minimum is often ``unpredictable", therefore most of the minimization algorithms (there are several depending of the software you want to use, see @Rajendra comments) are used to locate the local minimum.
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