after I got the pro-pro docking results , i try to use discovery studio and ligplot .but all of them recognise the result as Chain A and B , they can’t recognise which is ligand , how can i modify with the pdb file ? thank you
Not sure I fully understand your question…
Your complex (a protein-protein one I assume) has chains A and B. Ligplot is not made to analyse protein-protein complexes… (but dimplot which is part of ligplot is).
What are you trying to do?