If I am reading their website correctly- 2D ligand interaction diagrams are internal to Maestro https://www.schrodinger.com/Maestro with is free to academics.

Have you check the file type/internals? is the ligand label as such (appropriately)? If they are not correct you will probably have trouble with most programs (or at least any set to search your file explicitly for ligand).

I'm not sure, but if your saying that you ligand is a peptide, you have two options for entry types:

1) as regular peptide: be sure it has its own unique chain name, (I don't know if LigPlot handles peptides entered as normal chain-sequences -- check the manual)

2) as a ligand; PDB, cif, etc have a different mode of data recording that open to any chemical structure (as opposed to know standard types like common amino acids) ligand are small molecules are always in this format, and many ligand specific programs will only accept this as an valid input.

Be sure the format is acceptable to the program you end up using.

Dear Zarrin Basharat

Similarly, DIMPLOT module can't identify peptide ligand. For LIGPLOT module, peptide ligand was separated, this PDB was generated form Discovery Studio software. 

Dear Jacob Pessin

Thank in your advance. For academic version of Maestro, I was requested since yesterday, waiting for approval. 

I'm sure in my pdb file because I was generated from Discovery Studio (DS) and in detail of this files. DS was generated peptide ligand as chain C (as shown in figure).

{Caveat: I'm not particularly familiar}

It seems to read only a single chain -- you can either manually enter the regions to examine in the fields on the right, in the format postion#-postion# ChainLetter (& additional region) as per the example in the window.

Or format the file so that the ligand is listed as a separate chain Ex. 'receptor' = Chain A, 'ligand' = Chain B

I'm apologize in technique. I'm not sure, how to edit in this file. Can you edit this files, please?, I attach pdb file with comment. Thank you very much

Thank you for all suggestion. Now, I can solve this problem, because Discovery Studio may be some problem when merged pdb files between protein and ligand. So, I was used Molsoft Browser for merge files and I can use merged-pdb file with Ligplot without problem. Furthermore, I was obtained Maestro academic version from Schrodinger and It's very good when try to use 2D ligand-protein interaction.

I have tried with maestro but it could not generate ligand interaction diagram for peptide ligand. If any suggestions for the same.

You may use BIOVIA Discovery Studio visualiser for the same.

You can use discovery studio visualiser software