Good Afternoon researchers,
Hello, I am working on a protein, I need to know where the metal (Cu) will bind to it, after that to the formed protein-metal complex , I need to do ligand docking to that region.
So my concern is how to do that using Autodock Vina.
In Autodock4.2, one can include the parameter for metal in AD4_parameter.dat and build the map files. Using these map files, docking with Autodock can be carried out. The parameters for additional metal atoms other than default metal atoms are available on Autodock home page. However, I don't know much how metal atoms can be parametrized in Vina.
I don't know if I am correct but as per the objectives of your work, as you know exactly where Cu binds, you can manually build the complex of protein-Cu. Now use this complex for docking with ligands. Such docking protocol may be analogues to one where HOH or few metal atoms are kept in binding site and docking is carried out.
If someone knows how this can be done with Vina, I am also interested to know.
Regard's
Rajesh Patil
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