I bought a set of Earnie Ball Beefy Slinky's. And I was wondering if the thick strings could have any kind of bad effect on the neck of my guitar if I play mostly in drop D? The gauges go from .54 to .11.

I was just wondering because the strings probably have a lot more tension but is it enough to do damage to the neck of my guitar?
You should be fine. You may need to adjust the truss rod and maybe the action, but nothing seriously bad will happen.
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I use an .11 set in standard tuning, won't hurt a fly so long as the intonation isn't done by a monkey.

.12s/.13s still don't have a bad effect on guitars so long as the intonation is decent. I do know for a fact they like to pull into Eb on their own, though.
I have the same set on one of my guitars that gets changed from Eb to C# tuning and everything in between, they should work fine for you.
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