Section 3.3.3.3.3.  CHARMM

This system, due to Brooks et al. (1983), is primarily concerned with molecular dynamics but it includes the capability of model-building proteins and nucleic acids from sequence information and values of internal coordinates (bond lengths, bond angles and dihedral angles). The resulting structure (or a given structure) may then be optimized by minimizing an empirical energy function which may include electrostatic and hydrogen-bonding terms as well as the usual van der Waals energy and a Hookean treatment of the covalent skeleton. Hydrogen atoms need not be handled explicitly, groups such as —CH₂— being treated as single pseudo atoms, and this may be advisable for large structures. For small or medium proteins hydrogens may be treated explicitly and their initial positions may be determined by CHARMM if they are not otherwise known.