Initially input is read from the terminal (Fortran logical unit #5). In general, data will be entered by either typing it into the script for the batch job or placing it in a text file and using the INCLUDE command to bring it to the attention of the program.
You are allowed to arrange your data in any fashion you wish. You can enter it all directly in the script or can separate different types of data in different files. Some kinds of data are consistently stored in separate files -- All the coordinates are stored together in a file and called ``the coordinate file''. However even this is not required. Sometimes it is useful to separate the coordinates into several files and bring them together at the last minute. Whatever the structure of the data TNT will interpret it the same way.