See https://cluspro.org/help.php :

Read the paragraph under:

"I only see my receptor in my results. Where is the ligand?"

I think the program returns the result as a multi-state object. In PyMOL, select "Show all states" in the Movie Menu to see all states,

or specify

split_states object

To get the two components as separate objects

If this does not work, I would have to see your output file to further diagnose the problem.

Thank you very much dear mam for your suggestions. It worked well and I got those missed atoms.

perfectly answered by Annemarie Honegger madam. I hope, your tri-peptide has only the standard amino acids