How does Molecular Mechanics represent and handle hydrogen bonds?
A. MM2 includes Hydrogen Bond interactions “automatically” by recognizing the nonbonded interactions between certain atom pairs as hydrogen hydrogen bonds. Special parameters are assigned to the interactions of these atom pairs (to distinguish them from ordinary van der Waals type of nonbonded interactions). Therefore, it is usually not necessary to explicitly represent hydrogen bonds. You may also verify that the particular atom pairs are classified as hydrogen bonds by examining the “Molecular Mechanics Details” file, where all the hydrogen bonded atoms are listed. Q.
