Hi Seshank,

You have a protein with a net charge that you want to simulate, is that right? The usual approach would be to add a counter ion to the system to neutralise the protein (typically Na/Cl).

I typically simulate proteins with 100 mM NaCl, and choose the exact numbers of Na and Cl ions to neutralise my protein (e.g. if I have a protein with net charge +2, add two more Cl ions than Na ions).

Also remember that histidine residues have 3 different protonation states that are accessible at physiological pH, so you'll need to think about which one you're going to choose and why (or simulate all 3).

The real problem is that charge of my system is 3.4599. if the charge is  integral it would be easy to add ions. But is non integral and adding ions in leap module is throwing this error. I have mutated a residue in my protein (arginine to histidine) and i think so it is creating the problem. Can any one help!!