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2. How to run LIGPLOT

To run LIGPLOT with HBPLUS

To run LIGPLOT, with all hydrogen bonds and hydrophobic contacts computed by HBPLUS, type the following:

ligplot filename [residue1] [residue2] [chain_id] [-h]

where:

filename is the name of the file containing your protein structure and should contain the full path unless your structure is in the default directory. The file must be in full Brookhaven Format (see Appendix A).

[residue1] and [residue2] is the residue range for the ligand.

[chain_id] is the ligand's chain identifier (optional).

[-h] indicates that you would like to enter a heading for the output plot (the program will prompt you to enter the heading).

This assumes you have installed both LIGPLOT and HBPLUS according to the installation instructions.

For example, to run a LIGPLOT for 6tmn, in which the ligand has a range of 1 to 4 with chain identifier I, you might type:

ligplot /data/pdb/p6tmn.pdb 1 4 I

Alternatively, if the ligand range is unknown, you can omit the optional parameters and enter:

ligplot /data/pdb/p6tmn.pdb

In this case, the program will search through the PDB file 6tmn and will produce a list of chain and ligand ranges. It will then prompt you to enter one of these residue ranges as the ligand.

LIGONLY - running LIGPLOT on its own

ligonly filename [residue1] [residue2] [chain_id] [-h]

The parameters are as before.

The LIGONLY script is also useful where you have just run LIGPLOT and now want to generate a new plot (say having slightly modified the parameters in the ligplot.par file - see section 5). This saves running HBPLUS and recalculating all the hydrogen bonds and hydrophobic contacts.