I too suggest the Taubes book Good Calories, Bad Calories especially if you're taking a university course in nutrition (it's quite a scientific book).
I have never understood the Atkins strict rule against caffeine. I've read several editions of the Atkins diet and it's never been explained to my satisfaction.
I don't actually follow Atkins myself - I came to low carb via Gary Taubes and I try to keep my carbs very low (20-35g) most of the time. Since I don't claim to be an Atkins adherent, I'm free to do as I choose, and I do use caffeine (not huge amounts). From what I've seen on these boards & some other ones I follow a large proportion of Atkins followers don't give up caffeine and they're still successful.
Recent studies saying that coffee may reduce risk of diabetes & some cancers (it's a powerful antioxidant) help me be more convinced that unsubstantiated recommendations against caffeine are maybe not-so-right (not just Atkins -- lots and lots of diet books recommend dropping caffeine).
In the end, in my opinion, the only way that you really make any diet successful long term is to adapt it to what you can live with happily. You can only make yourself suffer for your weight for so long -- the permanent approach will have to be something you enjoy.

