I synthesis new ligand, that ligand react with divalent metals it forms metal complex. l used maestro 9.0 for docking the protein with ligand but the problem was maestro 9.0 (not only that all the docking software) not accepted the coordination bond between the metal and ligand in the .mol or .sdf format.so how to dock metal complex with protein.
Alisa Gorislav
There are some ways to dock with metal ions:
- Here is a Maestro tutorial - maybe you could find in useful - https://support.schrodinger.com/s/article/785
- There is an option to switch software and use AutoDock Vina - https://autodock-vina.readthedocs.io/en/latest/docking_zinc.html
- If your data is not private you could also use public server -
Article MIB: Metal Ion-Binding Site Prediction and Docking Server
+ http://combio.life.nctu.edu.tw/MIB2/
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