Well, PDF may be the worst format to convert, but that doesn't mean you can't, merely that it will probably require some TLC to fix it up after converting.
Check the sticky on the subject in the calibre ==> Conversion subforum, then apply some of the tips to converting the PDFs you have. Alternatively, you might simply use k2pdfopt to reflow the PDFs, which can make it dramatically more pleasant to read on your Kindle.
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