Hi,

you have to add this to either the AD4.1_bound.dat or AD4_parameters.dat (often found inside MGLTools directory):

atom_par Pd 1.34 0.048 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding

Also, as it is VINA, you might have to recompile it again.

Ok sir, thank you for your reply.

Hi,

Please guide...how to resolve the following error in MD simulation using AutoDock Vina:

"Parse error on line 32 in file "ligand.pdbqt": ATOM syntax incorrect: "Be" is not a valid AutoDock type. Note that AutoDock atom types are case-sensitive."

Thanks.

Hello sir,

Auto dock Vina did not read some elements, by default only some elements are there so, you can go with another software to dock.