3. Inputs to LIGPLOT

The input files to LIGPLOT are:

filename.pdb - Input PDB file holding the coordinates of the protein and ligand. See Appendix A for definition of file format (Bernstein et al., 1977).
filename.hhb - List of hydrogen-bonds in the structure. This can either be generated by the HBPLUS program (see McDonald & Thornton, 1994), or supplied by any other program in the format specified in Appendix B.
filename.nnb - List of nonbonded contacts in the structure. Again, this can either be generated by the HBPLUS program, or supplied by any other program in the format specified in Appendix B.
ligplot.prm - Parameter file containing parameters governing the final appearance of the plot. It is automatically created when you first run LIGPLOT. It can then be edited using any text-based editor to alter the parameters controlling the appearance of the plot - eg colours, text sizes, etc (see 5. The ligplot.prm parameter file).

And, optionally:

filename.rcm - List of positional restraints on the residues plotted. The file contains a list of centres of mass (x-y coords) for each restrained residue, relative to the ligand (at the origin) (see 6. Improving the plots - Same protein different ligands).

Note that, for the PDB file, the file extension does not need to be .pdb. It can be anything other than .hhb, .nnb or .par. The extensions for the .hhb and .nnb files must be as stated, otherwise LIGPLOT will not be able to find the files.

Furthermore, you should not use the filename "ligplot.pdb" as the input file unless you want to merely regenerate a plot (perhaps after manual modification on the graphics) as described in section 6. If the input name is "ligplot.pdb", the program does nothing to the coordinates except print them straight out as they stand.