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From @tfoote's answer for a very similar question:

to use Anaconda you will need to do a lot with your PYTHONPATH to make sure that all dependencies are on the path that Anaconda's interpreter is using.

I would recommend trying to find a way to use anaconda separately/in parallel with your anaconda installation. The main problem is that Anaconda doesn't use the standard installed python libraries so often you end up with missing resources.

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