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The Basal Metabolic Rate and Calories Burned calculators on the Internet are all based on bodyweight. I weigh the same now as I did back in college, but my bodyfat is higher. :( I'm pretty sure that means my BMR and calories burned during activies have decreased. What should I put for my weight: total weight, lean mass (i.e. bodyweight * (100% - % bodyfat)), or weight @ a specific bodyfat percentage? I'm trying to calculate how many calories I need per day and then cut it down from there.
That's pretty perceptive...your BMR probably is different now.
If you're using one of the calculators based on the Harris-Benedict formula, it takes into account your age, and makes some adjustments based on that. While there may be some formulas based on body fat percentage, I'm not aware of them, and doubt they would be much more accurate than Harris-Benedict (because body fat is also an estimate).
Bottom line: use one of the age-adjusted formulas, set an appropriate calorie goal (500 calories less than your estimated "active" metabolic rate), and monitor your weight over time. If you're losing at a reasonable rate (around 1 lb per week +/- 0.5 lb), you'll know you're dialed in. If you're losing weight faster, eat just a bit more. If you're not losing weight, back off a bit on the food consumption.
This assumes, of course, that you've got a reasonable exercise program in place too.