You can use the academic version of maestro in Schroedinger package.

I had encountered the same issue, you need to edit the file manually in word pad. Afterwards, you have to delete the model 2 (or any number) written before the coordinates of the ligand. Thus your ligand will be visible and then go to view interaction module to check the interactions.

Thank you Anu Manhas for replying. I tried deleting numbers in front of coordinates but that didn't work.This is my pdb file. Could you please tell which parts I should delete?

Yea sure, Let me see.

You can defined Ligand there itself,, Just need to assign differnt names.

Here im attaching the file ., note that i deleted the water molecules and added the hydrogen atoms, you need to verify those. Further, i could not find any dominant interactions such as hydrogen bonds, hydrophobic or non-bonded.

Please look into the attached PDB files, now you will be able to see the inhibitor and its interaction. Remember discovery knows ATOM and HETATM only and can distinguish a inhibitor from amino acids if you mention the inhibitor as HETATM.

Which software you have used to perform molecular dynamics simulations?

I hope this will be helpful for you.

Thank you Anu Manhas and Nikhil Maroli . @Anu Manhas I used GROMACS to perform molecular dynamics.

The file Anu uploaded do not contain proper hydrogen atoms, one need to add hydrogens before performing any analysis and around 5 A radius of the ligand i could not find any interactions.

Actually, I was focused on the above mentioned query " But I can't view the ligand through DS visualizer. It says my ligand is undefined."

Here is one more attached file incorporating the hydrogen atoms. Moreover, I had edited the file manually.