As advised above, you need to calculate your water treatment (as always) to get the right mash pH. If you won't have the roasted grains in the mash, you are essentially calculating for a pale grist that won't need alkalinity. Bru'n Water has a selection at the bottom.of the grain bill input that allows you to reserve roasted grains from the main mash. This allows you to calculate the color, while not miscalculating the mash chemistry. If you want some alkalinity-contributing salts in the beer for flavor effect, you can reserve those and add them directly to the boil. There's advice on this somewhere in the Bru'n Water documentation.
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