@ Kshatresh Dutta Dubey Thank you for your detailed reply.
I did correctly till step 6. In hbond-details.dat, there are 6 hydrogen bonds. In Graphical rep, I did select them. But, I am not able to "visualize the hbond" as we do in PyMol.
@ Roshan Shrestha If I give drawing Method as Hbond, we are not able to visualize anything. The VMD window becomes blank.
@Xavier, first of all make a suitable graphical representations for both your ligand and protein like VDW or CPK for ligand and New cartoon for protein. Then, create another representation for your system like all or like [protein or ligand] (In this representation, you can choose Hbond for your drawing method).
@ Roshan Shreshta I tried as you said. I could see the Hbond. Now, my question is Hbond between proteins also appear. I want to see "only" Hbond between protein and ligand. To prove that the hbond between protein and ligand exists throughout the simulation run.
@Xavier, Now, it's upto you to make a clever selection in VMD for visualizing the Hydrogen Bonds between protein and ligand alone like protein within 5 of ligand or (sidechain and ligand) since you want to ideally study the Hydrogen bonds between the sidechain of protein and ligand and so on.
I have a docked structure of Antigen and Antibody (in a single PDB) and looking for some python based script (chimerax or pymol or gromacs or vmd either is fine) which can show the Hydrogen bond between antigen and antibody. Also I want to store the output file.