14.4 Internal Coordinate File Structure

The internal coordinate file can be stored in either card or binary form. for most purposes the card form will be used (since it can be edited). There are two types of elements in the internal coordinate file, those that correspond to normal dihedral angles and those that correspond to improper dihedrals. They can be distinguished by the presence of a '*' just before the iupac name of the third (k) atom (its presence denotes an improper dihedral type). For each element there are four atoms (referred to as I,J,K,L) and five values. The values for ordinary elements correspond to: R(IJ), THETA(IJK), PHI(IJKL), THETA(JKL), and R(KL) respectively. For improper dihedral types, the values are: R(IK), THETA(IKJ), PHI(IJKL), THETA(JKL), and R(KL). Notice that for the second type that the K atom is at the center of both angles. Elements of the IC file are symmetric with respect to inverting the order of the atoms except that for improper types only atoms I and L can be interchanged (also the sign of PHI must be changed since PHI(IJKL) = -PHI(LJKI).)