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Article in "Journal of Physics A"

Finally we decided the destination of our article. Since the results are mostly mathematical, i.e. graph theory, we decided to send it to "Journal of Physics A", statistical and mathematical physics. I've got a LaTeX template for my article, BUT it doesn't want to compile the stuff I wrote. I am trying already like 3-4 hours, but desperately. Disappointed. I'd like to know if it looks good in a journal or I should run the programs again (the second case is more probable) :( For now, as a draft, I use a template of ETH-Zürich, but, of course, one needs another form to be filled for the article. Maybe, somebody of you knows about the possible problems with  "Journal of Physics A" template?