In the standard version of LIGPLOT these files are automatically generated using the HBPLUS program. (They can alternatively be supplied in LIGPLOT-format from another program - see Appendix B). In the former case, using HBPLUS sometimes gives incorrect results as, when HBPLUS encounters a ligand it does not recognize, it may be unable to correctly calculate all the hydrogen bonds the ligand makes with the protein.
To get around this problem, you may need to define your ligand using the HBPLUS input format (see section 2.6 of that program's Operating Manual).
With v.3.0 of LIGPLOT comes a program called HBADD (described in Appendix C) which aims to generate such an input file for HBPLUS automatically. It makes use of the Het Group Dictionary, available from the PDB and relies on the atom-names and connectivities of the ligand atoms in your PDB file matching those in the dictionary.
If there is a mismatch, you may either have to rename your ligand atoms, or create an appropriate input file for HBPLUS.
An alternative, and possibly simpler way, is to run LIGPLOT, see which H-bonds it misses, and then add these in manually before running the program a second time. The procedure might be as follows:-