I think you are looking for protein-ligand conformation after docking has been performed right? You can use Chimera to create one pdb file i.e all of the docked posed in your protein could be seen in Chimera, or you can also use AutoDock GUI, it also provides you with the option to do so plus in autodock GUI the residue interactions in the active site can also be seen. Discovery studio visualizer is also an option.

In addition to the software that Danish suggested, I would also recommend PyMol, which you can use to combine both ligand and protein in 1 PDB file when you save it. Aside from that, you generate publication quality images with the ray tracing command (similar to what Chimera can do).

Hi Chanin Nantasenamat,

Thanks! Yes currently I am using PyMol. But I don't know how to combine the ligand with the protein as a single file. Do you know how to do that?

Hi Nor, unfortunately my Mac OS X was just upgraded to Yosemite and it had caused my PyMol to not load up properly.

I think you may also do this manually via a text editor. Since the ligand is docked inside the binding cavity the ligand should be in the same cartesian coordinates as that of the protein. I think you can just copy and paste the contents from the ligand.pdb at the end of the protein.pdb but just before the CONNECT and END syntax found at the last few lines of the protein.pdb file.

Dear Chanin,

It is solved now! Thanks to you!

However, I have another concern regarding the flexible residues. The pdb file of my protein also contains those flexible residues. What will happen if I combined them? The flexible residues from docking result will overlap with the ones in my protein pdb file right? How do I combine these?

How did you solve this problem? I am facing same problem. Please, reply.

Dear Sonia,

I chose my best ligand conformation from the Autodock GUI, then on the conformation player, I clicked on symbol '&' and choose 'write complex'. This will write pdbqt file of the protein-ligand complex. Then you can convert pdbqt to pdb.

If it doesn't work, save your ligand conformation as pdbqt first (by clicking on 'write current'). Then convert it to pdb. After that you can combine the pdb file of your ligand and your protein to generate the pdb file of the complex.

Hope it helps:)

http://prosciens.com/prosciens/oldproscienssarl/a-useful-script-for-autodock4-and-vina-that-gracefully-merges-flexible-and-rigid-pdbqts/

You have to saves rigid part as pdbqt when you prepare your files and then combine your output (docked pdbqt) with that rigid pdbqt. You can use PyMOL for this combination.

The best

Abdo

If anybody still have a problem, I suggest using my python3 script for merging, available on this github repo:

https://github.com/Rmadeye/vina-merger

or use web application:

https://protein-ligand-merger.herokuapp.com/

Best,

Rafal