I always had same problem with LIGPLOT. If you don't have to use it, my suggestion is using PDBsum webserver (generate madoule). It gives you a better representative of your molecular interaction than LIGPLOT.

Dear Eman Koosehlar, yes you are right. But when Uploaded my docked file ( using cluspro or patchdock) in PdbSum it shows only one chain, however, in pymol shows both receptor and ligand. I am really confused actually where I am doing wrong.

Eman Koosehlar Md. Sakib Hossen Within LIGPLOT+ program, you may use DIMPLOT to identify protein-protein interactions.

Prasanth Kumar, yes for protein-protein interaction I go to the Dimplot option, but it didn't show any chains at all, that's why I couldn't run.

Md. Sakib Hossen You may need to insert chain names separately by using PDB file by just giving this command (https://stackoverflow.com/questions/62399798/how-do-i-correctly-add-a-chain-id-to-my-pdb-file) or Pymol. Once you did, submit to PDBsum then.

@Prasanth Kumar problem solved, thank you so much.

Solution:

Open the PDB file on PyMOL and follow these instructions to add/alter the chain identifier:

select the chain for which you wish to add/alter the chain id

*make sure that the selecting state (on the bottom right side) is on chains

type the command: alter (sele),chain='A'

*This will alter the chain id to A, if you want another id change the command accordingly

type the command: sort

Open the file menu, click on Save Molecule, select the option 'sele' and save (give a new file name)

Hi Md. Sakib Hossen , I experienced the same thing in my work from cluspro and ligplot. However, I dont understand on the part on what chain need to be added/altered. I have also one file from cluspro that can be viewed from the ligplot but not dimplot option where in fact it is a protein-protein interaction. do you think it is acceptable?