when I try to compile my document in order to keep looking the format, i recieve the following error:

/usr/share/texlive/texmp-dist/tex/latex/base/utf8.def:39:TeX capacity exceeded, sorry [text input levels=15]\ProvidesFile{utf8.def}

It exits with error code 1 and does not create the pdf file. I put the code here.

Thanks for the help!



\title{Reconstruction of a macro-complex using interacting subunits}
\author{Lydia Fortea \and Juan Luis Melero}

  /Title    (Reconstruction of a macro-complex using interacting subunits)
  /Author   (Lydia Fortea \and Juan Luis Melero)
  /Creator  ()
  /Producer ()
  /Subject  (Structural Bioinformatics \and Introduction to Python)
  /Keywords (modelling, reconstruction, macro-complex, structural alignment, structural bioinformatics)



The aim of the project is to reconstruct a marco-complex having only the pair interacting chains, using a standalone program created by ourselves.
The program we created is based on several bioinformatic features, including modelling, structural superimposition and sequence alignment, among others.

\section{Protein-Protein Interaction and Complexes}

An important point of the project is understanding the Protein-Protein Interaction and Complexes. In the quaternary structure of a protein, there are more than one separated chains of proteins that interacti between them.
The interaction of these chains can involve a lot of intermolecular bounds, such as hydrogen bounds, electrostatic interactions, pi stacking, cation-pi interaction, etc. This diversity of interactions makes the protein-protein interaction
very common in order to stabilized the molecule and generate a biological function.

The whole structure, where two or more chains are combined and have one or different functions, is called a complex. The formation of a complex can be made by protein-protein interaction only or nucleotides (DNA or RNA) can also be part of a complex if there is DNA-protein or RNA-protein interactions.

Focusing on the project, having the protein-protein interaction by pairs, we want to reconstruct the whole macro-complex.

\section{Structural superimposition}

We cannot assume that the protein-protein interacting pairs are well oriented in the space. Therefore, in order to give to each part the correct orientation, we do a structural superimposition. 

\section{Complex Modelling}

Modelling is the process through which having a protein sequence and one or more templates we can infer the structure of the protein. This is made by a program called \textit{Modeller}. 

\chapter{Algorithm and Program}

\section{Inputs and Outputs}

\section{Modules and Packages}

\textit{Biopython} is the main package used, as well as \textit{sys}. 


Biopython is the main open-source collection of tools written in Python to work with biological data. From Biopython we take the following subpackages:

\item Bio.PDB, to work with PDB files
\item Bio.pairwise2, to align protein sequences one by one
\item Bio.SubsMat, to import Substitution Matrices to score the alignment


Sys package is the System-specific parameters and functions. This package is used to read the arguments in the command line (sys.argv) and to have access to the three channels of communication with the computer: the \textit{standard in} (sys.stdin), the \textit{standard out} (sys.stdout) and the \textit{standard error} (sys.stderr).


%We superimpose those chains that are the same. We know what chains must be superimposed because we did a previous sequence alignment and we superimpose those chains with a percentage of identity greater than 99%.

%Once we have the parts well oriented, we use each part
\section{Restrictions and Limitations of the Program}

\chapter{How to use the program}



\chapter{Analysis of examples}

\section{Proved examples}

\section{Generalisation of the program}

\chapter{Discussion of the project}





  • Welcome to TeX.SX! Please reduce your code to a minimal working example (i.e. remove everything that is not necessary for the problem to persist). – schtandard Mar 22 '18 at 9:21
  • (1) Welcome, (2) If you look in the log, you'll see that utf8.def is being loaded many many times. If I outcomment the \pdfinfo call, the error disappears – daleif Mar 22 '18 at 9:21
  • 1
    Welcome to TeX.SE! Just do not use \and in \pdfinfo ... – Kurt Mar 22 '18 at 9:21

This is caused by the use of \and inside \pdfinfo. Just use and or \& instead.

Also note that \pdfinfo does not play well with hyperref. If you want to have links in your document, you may want to consider switching to hyperref for providing the PDF meta data as well.

  • 4
    Now explain why the use of \and made pdflatex load uft8.def several times ;-) – daleif Mar 22 '18 at 9:25
  • 1
    @daleif: I do not know how exactly the \and causes LaTeX to load utf8.def multiple times. In my opinion, however, this is irrelevant to the OP's question, since the compilation would also fail without \usepackage[utf8]{inputenc} (with a different error). The problem here is that \and (i.e. \end {tabular}\hskip 1em \@plus .17fil\begin {tabular}[t]{c}) just does not make sense inside \pdfinfo. – schtandard Mar 22 '18 at 9:35

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