In all likelyhood your coordinates will start out in PDB format. The from_pdb command will convert PDB files to TNT files. Because the PDB format contains information which TNT stores in several different files the output from from_pdb will be a .cor file, a .seq file and a .tnt file. Each file will have the same name as your PDB file. If the creation of the sequence or control file would overwrite an existing file a new version is not created. That is, if you already have a TNT control file from_pdb will not create another.
Some programs write PDB files without including the cell constants. Cell constants are required for proper placement of the molecule in crystal's unit cell. You can provide the cell to TNT by either editing the PDB file or by creating a TNT control file containing a CELL statement (A prototypical TNT control file can be copied from $refroot/tnt/doc/prototype.tnt). You should also complain to the author of the offending program.
Because TNT places more information in its files than the PDB file contains you will have to edit some of these file. Usually the coordinate file will be okay. The sequence file might require some editing and the control file will require a great deal. These issues are discussed below.