The 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.

Open the complex in DSV (free). Use ctrl+H for viewing the hierarchy. drag the ligand chain with mouse and leave on the amino acid chain. Now if you want you can rename the chain as pro&lig. Then save the coordinates in pdb format. Now open in LigPlot, it will work.

Regards

Bikash

Osaka University, Jpan

Thanks for your reply Bikash, its working ........

To generate de the complexes you can use http://bioinfo3d.cs.tau.ac.il/PatchDock/. If you have the pdb archive, you can send it to http://www.ebi.ac.uk/pdbsum/ and analyse the interactions between ligand and the protein.

HI all

Can anyone let me know how to install ligplot and use it?

I kept the default directories but its not working

Its very simple. All the instructions are given in ligplot manual. dont forget to get the latest version of components.cif file. its link is also mentioned in the manual. 

Here is the URL for manual 

http://www.ebi.ac.uk/thornton-srv/software/LigPlus/manual/manual.html

find for .cif url for downloading components.cif file

Hi. I need help. I have run the LIGPLOT, but I keep getting error message ''LIGPLOT failed. File not found: C:\tmp\lig5519066766696727914\ligplot.drw''

Can you help me with this problem?

Thank you very much!

If your protein-ligand complex was built using autodock vina, you should make this manually. You could try the following:

1) Open the ligand_out.pdb;

2) Copy the best result of your model (below "Model 1 -6.7" up to "Endmdl");

3) Then, open the proteín.pdbqt (using word pad);

4) Paste the model's result above "end" in the protein.pdbqt

5) Save as .pdb

6) Finally, open the generated file.pdb using ligplot