[gmx-users] charged & uncharged ligand

[shahab shariati]

Dear gromacs users.

My system contains protein + ligand.

Total charge of my protein = 0

My ligand has -NH2 group.

I want to do 2 md simulations:

1)deprotonated state of ligand (-NH2).   =>  Total charge of system= 0

2)protonated state of ligand and (-NH3+)=>  Total charge of system=+1

I have no problem about the first simulation. I have a question about the
second simulation:

Should I one Cl ion to system using genion tool? I want to study effect of
the charged ligand on the protein.

Any help will highly appreciated.