7. Adding/removing H-bonds and hydrophobic interactions

LIGPLOT uses the list of hydrogen bonds supplied in the file filename.hhb, and the list of hydrophobic contacts supplied in the file filename.nnb (where filename is the name of the original PDB file).

These files can be automatically generated using the HBPLUS program, or otherwise supplied in LIGPLOT-format (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.

For this reason, or otherwise, you may want to add or remove interactions from either the .hhb or .nnb files.

One way, is to run LIGPLOT, edit the .hhb and .nnb files, and then run LIGONLY. However, the format of these files is a trifle cumbersome and awkward to edit.

A simpler way is to use the files ligplot.hhb and ligplot.nnb, generated in the LIGPLOT format when LIGPLOT is run. The file format is a great deal simpler, and also has the advantage of showing only those interactions that were actually plotted, rather than all possible interactions in the original PDB file.

Having edited in, or removed, the relevant interactions into either ligplot.hhb or ligplot.nnb, overwrite the original filename.hhb and filename.nnb files before running LIGONLY to regenerate the plot - this time with all the correct interactions shown.

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