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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 
. 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".
Xplor-NIH 2024-09-13