[gmx-users] Should Cation Ligand be removed before MD simulaiton

[Quin K]

Hi

I'm hoping to use a protein for MD simulation and later for docking with
Autodock vina.

*However there is a  Mg2+ cation ligand in the DPB crystal structure of
protein. Should this be removed before MD simulation? *and replaced with
lets say Na+ to keep the charge of protein zero.
I'm hoping to use the protein for a drug molecule docking later.
Also hoping to do MD simulations for complex of drug molecule and protein.

Thanks!
Regards!