@Lukun There is lots of required information missing here to give competent and meaningful suggestions.
How did you do that? Manually? Or through LAMMPS? Considering periodic boundaries? with/without using a long-range Coulomb solver?
One has to be an mind reader to know exactly what you did, and without knowing that one cannot tell you what you did wrong. Since you are talking about a tiny system, you should provide all details and explain what you computed how so that we can actually see what you did and also show what you computed with LAMMPS, and - perhaps - then it is possible to tell you what you did wrong.
How large is this non-zero charge? Sometimes this is just due to rounding, sometimes due to imprecise input. sometimes an indication of an incorrect input. Again, without actually seeing the files you use and the output you got, it is next to impossible to make a meaningful assessment of the situation.
I have already pointed you toward the forum guidelines and have to do this again. Your chances of getting meaningful and useful advice strongly depends on how well you follow the suggestions presented there.