Not really familiar, sorry about that, 

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

check point: 2. After installation

the first time you use it you have to define a few paths.

1. First of all check your licence expiry date.

2. If you downloaded it recently then check the java appropriate version is installed on your computer or not ?

3. then install it on your computer.

4. download the components.cif file and paste them in to the data folder of pdbsum.

5. Click on Edit menu and set the few program paths installed at specific location on your compouter (components.cif , temp folder, rasmol or pymol program) .

You should to check the pdb file and make sure that the chain id and the residue number are all at the right column, especially the ligand.

whould any one guide me to install ligplot from the 1st step, i always fail, Thank you

Hi,

As Filippo Prischi said, when you are installing Ligplot for first time you have to define path for the temporary file to be stored. So in the 2 line its written c:/tmp. therefore create a new folder in your C drive and name it as tmp. save this and Voila!!!!!

As mentioned, setting the path is crucial where I too faced some error.

I believe the provided instruction for installation is already crystal clear:

( https://www.ebi.ac.uk/thornton-srv/software/LigPlus/install.html)

Here I'll try to summarize the system configuration (setting path) on the first time run:

Hope this help!

I solved this exact problem by first, creating the input .pdb file for ligplot as followed:

1. Open the enzime and the docking result from autodock vina (all conformations of ligand)

2. Save (save molecule) the specific ligand conformation that you chose. Close pymol

3. Open Pymol again and open the protein and also open the specific ligand conformation that you just saved.

4. then click on save molecule and select both the protein and the ligand. Close pymol

5. Finally, open pymol again and open the file saved on point 4. Then click on export molecule and select .pdb. This is the file that will run on ligplot solving the error. Nor Hasmaliana Abdul Manas