Question: What could be the reason that the hydrogens disappear from the ligands after the docking simulation in Autodock
0
gravatar for Neha shri
3.5 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 • 1.5k views
ADD COMMENTlink modified 3.4 years ago by Chris Cole680 • written 3.5 years ago by Neha shri30
0
gravatar for Chris Cole
3.4 years ago by
Chris Cole680
Scotland
Chris Cole680 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 3.4 years ago by Chris Cole680
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