CHARMM “toph11.dna" and “param11.dna" Files for Nucleic Acids (Explicit Polar Hydrogens)

This force field, described by Brooks et al. (1983), treats only polar hydrogens explicitly. It uses the explicit hydrogen bonded energy term (Eq. 4.25). For crystallographic and NMR-spectroscopic structure determination, it may be necessary to restrain the sugar pucker by using the restraints dihedral statement (see Section 7.2). Furthermore, it may be necessary to increase the energy constants of the improper angles to ensure planarity of the bases.