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It's just I'm having a really hard time getting started with AutoDock and I was wondering if it would be appropriate for me to ask questions about it here and if not which stackexchange website would be best suited for such questions.

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In general, http://stackoverflow.com is best for software/coding questions. However, there only seems to be one or two quesions on AutoDock there, so you will most likely not get many answers. You could try here at BioSE or https://chemistry.stackexchange.com/ as well (I dont know exactly what the program does), since there might be other users of the program that can help. However, questions like "How do I import this data into that program?" is not really a question about biology (or chemistry), and would be off-topic. In any case, your first stop should be the program documentation and you should also use support/contact info/forums directly connected to the software.

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Bioinformatics questions are fine here but only if they concern the underlying biology ("how can I identify genes in a novel genome" for example). This question sounds like it is more about using a particular program and, as such, would be off topic here.

I am not active on chemistry.se but I would imagine it is off topic there as well. You could ask on stack overflow as suggested by fileunderwater but the best place would probably be http://biostars.org. That site is not part of the SE network but has a very similar system and is devoted to bioinformatics.

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