Returning Member

Retirement tax questions

I am having the same issue.  I converted $45,000 from a Traditional IRA to a Roth IRA.  I expected to pay the taxes, but Turbo Tax is telling me that I owe 6% on the excess over the annual contribution limit of $6,000, which is $39,000, thus the penalty I have to pay is $2,340.  This is not a contribution, but rather a conversion.  Why does Turbo Tax continue to say I owe the penalty?  I don't want to file my taxes until this is corrected.  What can I do?   Please help!!