After setting the box with editconf I the system had a charge of 16. Does anybody know what happend? How do I have to handle uneven charges, can I added 1.6 counterions? I don't think so.

I assume that you meant to put 1.6 both times, not 16?
What is your system?
What is your forcefield?
If you have many different parts, which part has the non-integer charge? (You could remake your system one piece at a time and look at the charge)
If you have a protein, how have you handled the N- and C-termini?


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