Carbohydrates constitute a structurally and functionally diverse group of biological molecules and macromolecules. In cells they are involved in, e.g., energy storage, signaling, and cell-cell recognition. All of these phenomena take place in atomistic scales, thus atomistic simulation would be the method of choice to explore how carbohydrates function. However, the progress in the field is limited by the lack of appropriate tools for preparing carbohydrate structures and related topology files for the simulation models. Here we present tools that fill this gap. Applications where the tools discussed in this paper are particularly useful include, among others, the preparation of structures for glycolipids, nanocellulose, and glycans linked to glycoproteins. The molecular structures and simulation files generated by the tools are compatible with GROMACS.

Laboratory of Physics Tampere University of Technology P O Box 692 FI 33101 Tampere Finland

Laboratory of Physics Tampere University of Technology P O Box 692 FI 33101 Tampere Finland Department of Physics University of Helsinki P O Box 64 FI 00014 Helsinki Finland

Laboratory of Physics Tampere University of Technology P O Box 692 FI 33101 Tampere Finland Department of Physics University of Helsinki P O Box 64 FI 00014 Helsinki Finland MEMPHYS Center for Biomembrane Physics University of Southern Denmark 5230 Odense Denmark

Laboratory of Physics Tampere University of Technology P O Box 692 FI 33101 Tampere Finland Institute of Organic Chemistry and Biochemistry Academy of Sciences of the Czech Republic Flemingovo nám 2 16610 Prague 6 Czech Republic

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