Files “parallhdg.pro" and “topallhdg.pro" for NMR Structure Determination of Proteins (All Hydrogens)

The weighting among bonds, bond angles, planarity, and chirality reflects the special requirements when using interproton distance restraints. Special improper terms have been added to maintain the trans- or cis-peptide bonds, chirality of all tetrahedral centers, and planarity of peptide bonds and aromatic rings. The peptide bond conformation is described by an improper angle that constrains the conformation to trans. The patch CISP allows the user to switch a trans- to a cis-peptide bond. The patch LTOD allows the user to switch from L to D amino acids. The peptide-bond linkages (Section 3.7.3) are defined in “toph19.pep".