Anaconda, running on El Capitan, only provides access to files and folders under the current user’s home directory.
My Dropbox folder lives on an external drive and therefore isn’t accessible from the folder list. (I actually use a slimline 128 GB JetDrive card from Transcend.. fast enough for my 100+ GB of Dropbox files).
The solution was to create a symbolic link in my Documents folder which referenced the external Dropbox folder.
$ ln -s /Volumes/SDCARD/Dropbox ~/Documents/DB
From Anaconda’s perspective this looks like any other folder: