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3. Inputs to LIGPLOT

• filename.pdb - Input PDB file holding the coordinates of the protein and ligand.

• filename.hhb - List of hydrogen bonds, either generated by HBPLUS, or supplied in LIGPLOT format (see Appendix B).

• filename.nnb - List of non-bonded, hydrophobic contacts, either generated by HBPLUS, or supplied in LIGPLOT format (see Appendix B).

• ligplot.par - Parameter file containing parameters governing the production of the plot (see section 5).

Note that, for the PDB file, the file extension does not need to be .pdb. It can be anything other that .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.