The TOPAS User Guide is now hosted in a hyperlinked rich text format by ReadTheDocs:
http://topas.readthedocs.org

They also host a PDF version:

For archival purposes, versions of the user guide from before we switched to ReadTheDocs are available below, but please use the above ReadTheDocs version as it is the most correct and up-to-date:
SelectionFile type iconFile nameDescriptionSizeRevisionTimeUser
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  3943k v. 1 Aug 10, 2016, 6:31 PM Joseph Perl
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  3963k v. 1 Aug 10, 2016, 6:31 PM Joseph Perl
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  3992k v. 1 May 27, 2016, 10:51 PM Joseph Perl