LIGPLOT frequently asked questions
Below are some frequently asked questions about installing/running LIGPLOT.
1. The PostScript output file only shows the ligandThe most common reason for the plot omitting the interacting protein side chains is that the program is not being run correctly.
The program should be run via the supplied command/script files. These files will take care of everything for you (namely running HBADD, HBPLUS and then LIGPLOT with all the correct parameters). On Windows the command file is called ligplot.cmd, while on unix-like systems it is ligplot.scr.
The installation instructions describe how to set up the aliases you need to run the programs via these script files.
If you are using bash, you need to additionally set up some export commands in your .bashrc file (see Running LIGPLOT under bash below).
If you are running the programs correctly, via the scripts, but some interactions, or even parts of your ligand, are missing, see the next question.
2. LIGPLOT doesn't work on my docked structureThe most likely reason is that your PDB file is not in the correct PDB format. It is quite astonishing how many well-known docking programs seem unable to output a correctly formatted PDB file - particularly for the ligand atoms.
The most common error these programs make is to name all carbons "C", all nitrogens "N" and so on. PDB format requires that the atoms in each "residue" be uniquely named. So your carbons should be renamed "C1", "C2", "C3", and so on. You can write a simple script to fix this.
The correct PDB format for atom records is given here.
3. When I run HBPLUS I only get .hb2 and .nb2 filesThere is no need to run the HBPLUS program. As mentioned in the answer to the first question, the LIGPLOT programs are run using the supplied command/script files. These files take care of everything for you (including running HBADD, HBPLUS and then LIGPLOT with all the correct parameters).
4. Is LIGPLOT available for Mac OSX?As the LIGPLOT source code is supplied it can be run on a mac providing you have a C compiler.
The only minor difficulty is that the default shell on a mac is bash, whereas the LIGPLOT scripts that run the programs use the C shell. See the next question on how to deal with this.
5. Running LIGPLOT under bashLIGPLOT is run via the supplied script files which use the C shell. The installation instructions tell you how to create a number of aliases in a file called .cshrc in your home directory to allow the scripts to run.
However, under bash, you also need to define the same aliases in your .bashrc file, which also lives in your home directory. The difference is that bash doesn't understand the command alias; you need to use export instead.
When I compile the programs I get a complier warning about the gets functionSome compilers give a warning along the lines of: "the `gets' function is dangerous and should not be used". This is just a warning and can be safely ignored. The function is never actually called when the program is running and, in fact, will be removed in the next version of LIGPLOT.
Last modified: 18 March 2010