Question: What could be the reason that the hydrogens disappear from the ligands after the docking simulation in Autodock
gravatar for Neha shri
4.8 years ago by
Neha shri30
United States
Neha shri30 wrote:

Hello everyone,

I am trying to analyse the interaction between a protein and some synthesized compounds. I have drawn the compounds in Argus lab, added the hydrogens and then used them for docking.

The problem is when i compare the ligand pdb file and the complex pdb (receptor and ligand) after the docking, i find most of the hydrogens missing from the ligand. Please point me to the probable reason for this. Will really be grateful. Thank you

autodock molecular docking • 2.1k views
ADD COMMENTlink modified 4.7 years ago by Chris Cole750 • written 4.8 years ago by Neha shri30
gravatar for Chris Cole
4.7 years ago by
Chris Cole750
Chris Cole750 wrote:

It's been a very long time since I did any of this, but I seem to remember that Autodock only used heavy-atoms during docking hence why you lose the hydrogens.

Adding the hydrogens back should be easy in any molecular graphics program.

ADD COMMENTlink written 4.7 years ago by Chris Cole750
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