I'd call your doctor and tell him/her that you already TOOK amoxicillin. Knowing that he/she might not have prescribed the augmentin in the first place.
Personally, I'd take the amoxicillin just because it is super bad practice to stop one antibiotic in the middle (not taking it the full term, I mean), because it manages to mess you up but doesn't manage to help. It is twice worse to start another antibiotic in the middle of the first.
In the case of Amoxicillin and Augmentin, however, the latter contains the former, thus an unfavorable reaction is unlikely. I would still check with the doctor, though, there could be something with the doses. (Augmentin is basically amoxicillin with an additive making it less successible to degradation (because there are organisms who can degrade the amoxicillin).
On the practical side, Augmentin is a very strong med and it is known to mess up normal stomachs. My mother took it last year and was miserable... it helped her, though, she had a bad case of bronchitis almost a pneumonia, and it took care of it completely. I have no experience with amoxicillin.
In conclusion, call your doctor and tell him what you did. It's not a wise idea to mess around with antibiotics. Make sure to let him/her know why you do not want to take augmentin.
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