The detailed contents of this file is explained in a latter section of this User’s Guide. It contains values for any of a wide variety of switches and parameters that are used to change the course of the computation from the default. key and is optionally present during Tinker calculations. The keyword parameter file always has the extension. The second list contains ``bonds’’ that are to be broken, i.e., pairs of atoms that are not covalently bonded, but which were used to define a distance in the atom definitions. These pairs are typically used to close ring structures. The first list contains pairs of atoms that are covalently bonded, but whose bond length was not used as part of the atom definitions. Following the last atom definition are two optional blank line separated sets of atom number pairs. The length, angle and dihedral definitions do not have to represent real bonded interactions. For each atom the internal coordinates consist of a distance to some previously defined atom, and either two bond angles or a bond angle and a dihedral angle to previous atoms. Each line contains: the sequential number within the structure, an atomic symbol or name, the force field atom type number of the atom, and internal coordinates in the usual Z-matrix format. It consists of a title line followed by one line for each atom in the structure. int file contains an internal coordinates representation of the molecular structure. Except for programs whose basic operation is in torsional space, all Tinker calculations are done from some version of the. Each line contains: the sequential number within the structure, an atomic symbol or name, X-, Y-, and Z-coordinates, the force field atom type number of the atom, and a list of the atoms connected to the current atom.
It contains a title line followed by one line for each atom in the structure. xyz file is the basic Tinker Cartesian coordinates file type. xxx is any of the several extension types to be described below. Then all of the Tinker files will reside on the computer under the name sample.xxx where. Assume that the file name chosen for our input and output files is sample. Let’s say you wish to perform a calculation on a particular small organic molecule. This section describes the basic file types used by the Tinker package.
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