My ligand is a metal complex conatining Ag (Silver). So when i tried to run Molecular docking using Autodock vina as well as PyRx, it shows error as
"Parse error on line 15 in file "Methioninesilver.pdbqt": ATOM syntax incorrect: "Ag" is not a valid AutoDock type. Note that AutoDock atom types are case-sensitive."
Any necessary recommendation to overcome this error.
You need to add Ag in the autodock file: refere here:https://autodock.scripps.edu/how-to-add-new-atom-types-to-the-autodock-force-field/
atom_par Ag 3.15 0.036 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding
Maybe this will be useful for you, in regard to do the step in previous answer
Hi Suraj, you will have to the edit the 'atom_constants.h' file in the vina install directory (given that you have installed vina from source). You will have to add the parameters of Ag in 'atom_constants.h' .
Adding new atom type in atom_constant.h is tricky.
To make things easy, you can rename Ag in your ligand to any metal which is recognized by vina (say, Zn, Mg, Fe etc.). Then you can change the parameter values of these metals in atom_constant.h file with that of Ag. The docking should then work fine. This is quite like dummy-atom approach.