I want to know some molecules charge in pH=7. but I think there's a bug in marvin view tools, because for example the charge of nh4+ should be +1 but marvin view says -2 !!! it is not possible. I checked these tool for some molecules and saw some conflicts. nh4 was the simplest!! I provided the procedure that I did in power point and attached it for you. the last slide is the output. please investigate it and reply me, because I really need to know if I'm right, or there's a problem in my procedure!
By the way I have an academic research license.
Thank you very much for your attention.
I think you got confused with the notation you saw in the output on your last slide. %-1, %-2 etc. is not the charge of the microspecies, it is simply the number of the microspecies, so 1st, 2nd etc.
So in the case of the ammonia, the 2nd (green) microspecies is the major form (ammonium cation), as the pH is acidic. Therefore you will find the molecule mostly in a protonated state, with +1 charge.
If you set your pH range to (8,9) for example, the ratio of the ammonia present in the solution will be higher.
I hope this helps,