How can I count the Hydrogen Bond after docking by Autodock Vina through visualizing by PyMOL? Ligand consists of Oxygen, Nitrogen, Carbon and so on. Oxygen of Ligand binds with the amino acids of protein. How can I confirm that Oxygen binds with the hydrogen of amino acids. Expecting experts comments.
You can upload the docked file in PDB sum. It will be provide you the details of hydrogen bonds and hydrophobic interaction of the docked complex.
you can see interactions ( H-binding and hydrophobic ...) with auto dock tools.
Dear Arif,
Convert the docked complex (Protein-ligand) from your software to pdb format. Upload the file in the following link.
You will get the interactions with contact residues and bond distances.
I have attached a model file herewith.
http://www.ebi.ac.uk/thornton-srv/databases/pdbsum/Generate.html
You can view the pdb model in Pymol.
Otherwise if you get MOE docking tool, it has ligand interaction option, nothing like it!
You could also use UCSF Chimera to do that.
https://www.cgl.ucsf.edu/chimera/
you can import your complex in pymol. So you can select A (action) and after preset. In preset menu you can select ligand site after cartoon and you can visualize all the contacts that the ligand can produce with the protein including H-bonds.
Write the complex of best conformations in .pdb format and upload it to PDBsum through the link
http://www.ebi.ac.uk/thornton-srv/databases/pdbsum/Generate.html
Discovery studio visualizer 4.0 is a user friendly software by which you can count the H-bonds with distances. You can also visualize other interactions. Ligplus is another software by which you can visualize H-bonds, however you will be required to make a pdb file of the ligand-macromolecule complex.
Gem Dock is a good software for docking and analysis, or docking with vina and PyMOL viewer
Use analysis menu in MGL tools, Analyze -> Docking -> .dlg file..... Analyze -> Macromolecule -> .pdbqs (Autodock V3)/pdbqt (Autodock V4) file, Analyze -> Conformation -> Play conformations... Gives you a separate window, Click on & symbol, gives a another window their you select show hydrogens by checking a checkbox. Now go through each conformations it will give you a information about hydrogen bond between each atoms very specifically.
Hope helps
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