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The Atkins diet is a diet that limits the amount of carbohydrates in a person's diet. And what it is NOT the only way "to go to build muscle." You were misinformed. It's just a weight-loss diet that can be used successfuly while you train. It doesn't help you build muscle faster...it is proven to slow down muscle growth (dramatically, I'm not sure). Carbohydrates are essential to fueling your muscles before, during, and after you workout. You also need high amounts of protein, and calories, (beleive it or not) some fat too. If you want to build muscle...dont' worry about your body's fat content...Worry about that after you've made strength/size gains.
About dieting...
If you eat 6 small meals a day (instead of 3 big ones), your motabolism will speed up dramatically, so you will lose weight. It isn't natural for humans to eat only 3 big meals a day....it came about due to social reasons in societies. Do monkeys only eat 3 times a day? More and more, people are eating as little as only 2 big meals a day....and the quality of food is a whole other story. That is why our society is getting heavier on average every year.