Chitin is the second most abundant organic material in nature after
+ cellulose and its study is now of great interest in the field of
+ biocompatible and eco-friendly materials. Computational studies of
+ natural polymers such as cellulose and chitin are often hindered by
+ the practical difficulties in generating structures suitable for the
+ simulations. This has motivated the recent introduction of a cellulose
+ builder tool that generates coordinate, structure and topology files
+ for atomistic simulations of cellulose crystal polymorphs. Here we
+ present an analogous tool for chitin, the Chitin Builder tool, a
+ program that enhances the Visual Molecular Dynamics (VMD) environment
+ with the ability to generate coordinate and structure files of chitin
+ organic crystals. The program generates Cartesian coordinates and
+ atomic connectivity and structure files for crystalline structures of
+ chitin polymorphs
Chitin is a polysaccharide present in the exoskeleton and internal
+ structure of many invertebrates like molluscs, crustaceans, insects,
+ fungus, algae, and other related organisms
+ (
The possibility to generate atomic coordinates of the crystal
+ structures of chitin is important from both a fundamental and
+ practical point of view, since it opens the possibility to predict the
+ properties of chitin based materials and derivatives (mechanical,
+ thermal, interaction with solvents, etc.). Starting from the atomic
+ coordinates provided by crystal structures, it is possible to perform
+ Molecular Dynamics (MD) simulations of chitin and study its properties
+ and its interactions with other materials. However, to date, there are
+ only a few works that deal with all-atomic MD simulations of chitin
+ (
The lack of atomistic simulations of chitin is even more surprising
+ when we compare this situation with the case of cellulose, which is
+ the other most abundant polysaccharide. In the case of cellulose,
+ there are many atomistic simulation works, deriving the most diverse
+ features of cellulose from the known crystal structure
+ (
In this work we present Chitin Builder, a tool implemented as a
+ plugin of the Visual Molecular Dynamics (VMD) program
+ (
This plugin will greatly facilitate the process of generation of + input files (coordinates, structures, topology) for atomistic + simulations and we expect that it will fuel the use of these + techniques in the study of these materials. Future developments of the + plugin will incorporate the generation of crystal structures of other + polymeric crystals.
+The code is a plugin for VMD written in the Tcl/Tk v8.4 programming
+ language. It can be executed from a graphical user interface (GUI) or
+ from the VMD Tk console command line. The source code contains two
+ main parts: the code that calculates the atomic coordinates of the
+ atoms of the crystal and the structure and topology of the crystal and
+ code responsible for the graphical user interface (GUI). The
+ calculation of the atomic coordinates is made based on published unit
+ cells for the different chitin crystal allomorphs (see Methods section
+ in the User Manual for details). The program generates two main
+ outputs: a coordinate file (PDB) containing the position of all the
+ atoms in the generated structure and a topology file (PSF) containing
+ all the bonds, angles and dihedrals according to CHARMM36 carbohydrate
+ section
+ (
Details on installation of the software, the user manual and
+ examples of code use are provided in the
+
We acknowledge financial support from the Spanish Government + through the RTI2018-096273-B-I00 grant and the “Severo Ochoa” Grant + CEX2019-000917-S for Research Centres of Excellence awarded to ICMAB. + We also thank the Government of Catalonia (AGAUR) for grant + 2021SGR01519. D.C. Malaspina was supported by the European Union’s + Horizon 2020 research and innovation programme under Marie + Sklodowska-Curie grant agreement No 6655919. We acknowledge + discussions with Prof. Lars A. Berglund and Dr Yamila Garcia about + chitin materials.
+