Greeting Researchers,
I am trying to dock ligand with protein, But my ligand has Chlorine and Iron metal ion in it. So do we have to add the charges to it??.
If yes, how ??
Autodock Vina ignores user supplied charges and uses some kind of knowledge based scoring function for metal-interactions.
You could use Autodock 4 instead of Vina and calculate partial charges with Gaussian or any other QM software.
Is your chlorine ion part of your ligand or only a counter ion to compensate charges? If it is not part of your ligand, you should ignore it for docking experiments.
if necessary try to manual adjust or add charges ti the force field parameters file
Does it make AutoDock Vina less accurate than Autodock for iron metalloprotein docking with organic ligands (not Zn metalloprotein)?
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