CHARMM “toph19.pro" and “param19.pro" Files for Proteins (Explicit Polar Hydrogens)

This force field, as described by Brooks et al. (1983), treats hydrogen implicitly by modification of the parameter of the hydrogen antecedent, except for polar hydrogens such as $N-H$. In the latter case, the hydrogens are treated explicitly in order to obtain a more realistic hydrogen bond potential. This force field does not use the explicit hydrogen bonded potential (Eq. 4.25); i.e., the HBONds energy term will be zero. The hydrogen bond energy is part of the ELEC and VDW energy terms. However, the DONOr and ACCEptor statements (Section 3.1.1) are still present in order to allow the user to analyze hydrogen bonds by using the print statement (Section 5.1.1). The peptide-bond linkages (Section 3.7.3) are defined in “toph19.pep".