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I am writing Thesis. After all the chapters, I am including only one Appendix at the end of the Thesis without any sections. I want equation numbers of the Appendix as (A.0.1), (A.0.2), etc. And theorem numbers as Theorem A.0.1 , Theorem A.0.2 , etc.

Please reply me

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    Welcome to TeX.SE. Have you any MWE to show what you have and what you want? – Romain Picot Jun 23 '15 at 12:44
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    Welcome. I'm afraid we can't answer your question without more information about your document including the class and any packages you are using to manage sections/numbering in the thesis. Can you post a small, compilable document demonstrating the skeleton of your thesis and illustrating how you want this to work? Also, please edit your question title: on a site dedicated to TeX and friends, 90% of questions are about 'LaTeX typesetting'! – cfr Jun 23 '15 at 12:45
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    I don't know about theorems, but if you are using \appendix or the appendix package, the equation number changes automatically as "A.1" and so on. – MarcoG Jun 23 '15 at 12:47
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    zero counters do not look really nice – user31729 Jun 23 '15 at 12:55
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Not knowing what document class you are using I cannot guarantee that this will work. This example uses the book document class and the associated \appendix macro to establish that the author is finished with the book and is on to the appendices, subsequently each chapter is treated like an appendix. Also, you should heed the comment from @ChristianHupfer that "Zero counters do not look really nice," before incorporating this into your thesis.

You can achieve what you want by using \renewcommand to change \theequation label to reflect the various counters you want to display:

\documentclass{book}
\usepackage{lipsum}

\begin{document}
   \chapter{a chapter}
    \lipsum{1}

    \chapter{another chapter}
    \lipsum{1}

    \appendix
    \chapter{an appendix}
    % put the following line in your document in the appendix
    \renewcommand\theequation{\Alph{chapter}.\arabic{section}.\arabic{equation}}
    \begin{equation}
        E = m c^2
        \label{eq:relativity}
    \end{equation}

    \chapter{another appendix}
\end{document}
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