The superpose program of the Tinker program suite predicts the best possible superposition of two structures a and b and calculates the final residual difference (rms distance) between these structures. The superposition is achieved through minimization of the rms distance d between the two structures. The latter is calculated accoring to equation (1) for a number of centers n specified by the user:
In order to perform the fit the program requests the names of the two structure files as well as a keyword file specifying the force field parameters. After accepting the file names of the two structure files the program asks for (a) whether to use all atoms 1 through n for fitting of the two structures (option 1), or whether the user wants to specify pairs of atoms for fitting (option 2); (b) whether to include hydrogen atoms in the fit (yes or no); (c) whether to fit in mass-weighted or unit-weighted coordinates (M or U); (d) whether or not to write out the best-fit coordinates of the second molecule (yes or no); (e) a cutoff value for listing rms devitions to the output file (or the screen). A typical program call together with a complete list of arguments would thus be:
superpose file1.xyz file2.xyz 1 y U y 0.0
This will superpose the structures in file1.xyz and file2.xyz using all atoms in the systems (including hydrogens) in unit-weighted coordinates and generate one new file file2.xyz_2 containing the best-fit coordinates of the system in file2.xyz.