[gmx-users] How to introduce Mg2+ ions to system that are necessary for nucleotide co-enzymes?

[Hassan Aaryapour]

Dear Gromacs Users

I want to do an unguided molecular dynamics simulations (500ns) with GTP or
GDP ligands that place at a random location within a simulation box that
also contained my kinase protein. How can I add or introduce Mg2+ ions to
system that are necessary for GTP or GDP ligands? How much Mg2+ is required
for GTP or GDP molecules in a cubic box with -d 1.0???



Is it logical I add ions to a system with -8.99999 net charge using command
below?

# gmx genion -s ions.tpr -o conf-ion.pdb -p topol.top -pname MG –np 4
-pname NA -np 1 -nname CL



Thanks

Hassan