2. How to run LIGPLOT

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2. How to run LIGPLOT

The script file that runs LIGPLOT assumes the following:
  1. That you have installed the HBPLUS program in accordance with the Installation Instructions.
  2. That you have installed the Het Group Dictionary, as het_dictionary.txt, in the LIGPLOT directory, in accordance with the Installation Instructions.

If you wish to use a program other than HBPLUS for calculating hydrogen bonds and nonbonded contacts, then you will need to alter the script file that runs the LIGPLOT program, ligplot.scr, to take this into account. The files output by the program will need to be called filename.hhb and filename.nnb, respectively, where the name of your input PDB file is filename.pdb. Their format must be as defined in Appendix B.

a. Running LIGPLOT

To run LIGPLOT, type the following:


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:

To define the range more specifically, you can include the residue names as:




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

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.

b. LIGONLY - running LIGPLOT on its own

If you do not have HBPLUS, or wish to use your own list of hydrogen bonds and hydrophobic contacts (see Appendix B), you can run just LIGPLOT on its own by typing:

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.prm file - see section 5). This saves running HBPLUS again to recalculate all the hydrogen bonds and hydrophobic contacts.

c. Showing atom accessibilities computed by NACCESS

One of the options in the parameter file, ligplot.prm, allows you to shade the atoms in the plot according to their atomic accessibilities (see, for example, the plot of the Gly-Ala-Trp inhibitor of chymotrypsin). Solvent accessibilities can be calculated by running the NACCESS program.

(Note that, if you have a version of NACCESS earlier than v.2.1, it is recommended that you get the latest version from the NACCESS Web site).

The procedure is as follows: run NACCESS on your PDB file and then run LIGPLOT on the .asa file generated by NACCESS. Make sure that the option for showing accessibility shading is set to Y in the ligplot.prm parameter file.

When running NACCESS, you need to include the -f and -h options. The former defines that the "full" output format is required, and the latter states that HETATMs are to be included in the accessibility calculations.

So, your command might be:-

This generates a .asa file, and LIGPLOT should then be run on this .asa file in place of the original .pdb file.

That is:-

Note that, if LIGPLOT is run on an ordinary PDB file, the values in the B-value column will be taken to be accessibilities.

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