What could be the reason that the hydrogens disappear from the ligands after the docking simulation in Autodock
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5.4 years ago
Neha shri ▴ 30

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 • 2.3k views
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5.4 years ago
Chris Cole ▴ 760

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.

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