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Hi, I am very confused as to why my tax preparation software is telling me that I am subject to a 6% penalty for a Roth IRA contribution of $2000. My AGI in 2001 is definitely less than the AGI limit...

Besides what Pixy said, you also can't file married separately and contribute to a Roth. If you're absolutely positive you qualify (read IRS Publication 590 and be real sure), you can tell the program you did not make a Roth contribution and get the return completed. The only reason they ask if you contribute is to make sure you qualify and don't have a penalty. It isn't shown on your tax return (unless you don't qualify.)

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