3. Inputs to LIGPLOT
LIGPLOT Operating Manual
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:
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.
LIGPLOT Operating Manual