Hello everyone
Can I use Vina to dock analogues of nucleotides triphosphates into a polymerase active site coordinating Mg ions?
The ions are also typically in coordination with water molecules to satisfy their proper geometry.
Is it possible to do such docking while, at least, Mg ions are kept at the active site?
If not, is there any open-source docking tool to to such docking?
Check out the answers to this question: https://www.researchgate.net/post/How_to_Mn_based_metal_atom_parameter_add_to_autodock, they are also valid for other ions that are not recognised by default.
get the parameter file from http://autodock.scripps.edu/resources/parameters/AD4_parameters.dat/view and follow the instructions kindly provided by @Nur Aqilah Zahirah Norazmi
Also: answers to https://www.researchgate.net/post/how_to_add_Ni_parameter_in_autodock_42
https://www.researchgate.net/post/How-to-add-Cobalt-atomic-parameter-in-autodock-42
https://www.researchgate.net/post/How-can-I-deal-with-metals-in-protein-using-autodock
Annemarie Honegger Thank you professor for your time and effort.
Vishal Kumar Sahu
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