The TNT control file contains all the information required to describe your project which is not properly included in either the coordinate file or the sequence file. Since this is a ``none of the above'' situation it is hard to describe in a simple fashion what goes in this file. Basically, if you need to provide some additional information to TNT you will enter the data in the control file.
You never enter the name of your control file when you run a TNT command. All TNT commands presume that your TNT control file will be located in the current directory and will be the only file which ends with `.tnt'
The control file is easy to use and usually not very large. Each line begins with a keyword which describes the data which will follow. If the data will not fit on one line you may continue on the next line by terminating the first with a ` ' character (or alternatively a `-' which must be preceded by a space). You may add a comment by either starting the line with the keyword NOTE or placing the `#' or `!' character before the comment.
If some collection of data statements become too large to conveniently contain in the control file you may place them in a separate file. In this case you would use the INCLUDE keyword in the control file to cause the new file to be read. For example, if the new file were called rigid_body.dat you would add to your control file the line ``INCLUDE rigid_body.dat''.
The next section describes many of statements which can be placed in your control file. The TNT Reference Manual describes other possibilities but those statements will be used less frequently.