How to visualize hydrogen bonds between protein and ligand in VMD?

Hi Xavier, there is no automated way to visualize the H bonds, but using some basics in VMD you can easily visualize them.

1. Go to the Extension-->Analysis--> Hydrogen Bonds

2. In the Hydrogen bond tab, you will see, Selection 1, assign there protein, and in selection 2 assign the residue name or residue id of your ligand.

3. You will see there an option as Calculate detailed info for: enable here Residue pairs.

4. Write output to a file, say, hbonds-details.dat and run the calculations.

5. Open the file hbonds-details.dat by any text editor and you will see the Hbonds between ligand and protein.

6. Now select those specific pairs in VMD selection tools ( Graphical Representations), and you will visualize the H bonds between ligand and protein.

Hope it helps

You can get it easily through Hydrogen bond tab in the analysis section.

For the visualization of Hydrogen bonds alone, make a selection of protein and ligand in Graphical Representation and choose HBonds in Drawing Method.

@ 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 thank everyone for your informative reply.

@ Roshan Shrestha Thank you very much for your prompt response

@ Xavier No Problem, I hope it helped. Good luck ahead.

@ Roshan Shrestha I have a question. While studying hbond-details.dat, we observe, for example, ASP 131-Side-OD1, what is OD1? What does it mean?

Xavier, OD1 is the atom name which is called Oxygen Delta 1 in standard PDB database, it is one of the Oxygen in carboxy group in the sidechain

Ok. Thank you.

(1) Is there any link which provides the full form of those acronyms (like OD1, CG and so on...)?

(2) Have you analyzed DSSP? How do we get information about the conformation changes in the protein using DSSP?

I think Google is your best bet. Regarding DSSP, use VMD timeline and select secondary structure to perform DSSP Analysis.

Here is a video in which I tried to explain in details the hydrogen-bonds analysis of protein dynamics in vmd

https://www.youtube.com/watch?v=8gc6jzbImpc&feature=youtu.be&fbclid=IwAR0TydZib9w4F9uhptUbGF5-S1xyD5Ht8FgKVXABQHuBpLGSdts6yJ9ApGY

Hi Folks,

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.

Any recommendation would be appreciated.

Thanks in advance