This is a collection of scripts to construct randomly orientied and structured systems of carbohydrate polymer structures. It produces pdb/psf files that are needed for Molecular Dynamics simulations. Currently, it is only implemented for constructing the Methanochondroitin polymer but it can also be used for other carbohydrates after indlucing the necessary source files and some alterations to 01_polymer_generation.tcl .
All scripts are supposed to be run using VMD that can be downloaded for free from
https://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD
and then they should be executed as
vmd -e Example1.tcl
For conversions to input files for other MD engines (including GROMACS, LAMMPS, ...) please use topotools: https://sites.google.com/site/akohlmey/software/topotools Additional scripts for conversion can be found in Examples/Input_Conversions.