We have developed two novel visualization algorithms for carbohydrate molecules: Twister and PaperChain. For more information on the algorithms, see

• Visualisation of Cyclic and Multi-Branched Molecules with VMD, Simon Cross, Michelle M. Kuttel, John E. Stone, James E. Gain J. Mol. Graphics Modell., in press (2009)
• Techniques for visualization of carbohydrate molecules, M. Kuttel, J. Gain, A. Burger and I. Eborn, J. Molecular Graphics and Modelling, 25, 380-388, (2006).

We have implemented these algorithms into the VMD Molecular Graphics Viewer. Binary versions of this package for IRIX, Linux, Solaris and Mac OS X are available for download from:

http://www.ks.uiuc.edu/Research/vmd/alpha/withcarbs/

Please be aware that this is a test version of VMD and not a released/stable version. The "PaperChain" and "Twister" visualizations are listed under Graphics > Representations Press "Create Rep". Then under "Draw style", "Drawing Method", select "PaperChain" or "Twister".

If you which to use the PaperChain algorithm in publications, please cite the articles listed above.

- a CHARMM-type force field for molecular dynamics simulations of carbohydrates. We have altered the primary alcohol dihedral parameters of a carbohydrate force field for CHARMM (developed by Brady and co-workers) to produce realistic primary alcohol motion. This was performed by adjusting the dihedral angle force constants and tested by calculating the potential of mean force for the primary alcohol rotation in both glucose and galactose. In addition, anomeric free energy difference calculations and vibrational analysis have been performed on glucose to further test the force field. The new Carbohydrate Solution Force Field (CSFF) may be downloaded:

Parameter file: CSFF_parm.inp
Topology file: CSFF_top.inp

For further information, refer to:

• Carbohydrate Solution Simulations: Producing a Force Field with Experimentally-Consistent Hydroxyl Rotational Frequencies and Populations, M. Kuttel, J. W. Brady and K. J. Naidoo, J. Computational Chemistry, 23(13),1236-1243 (2002)

• Developing Novel Molecular Visualizations for Complex Molecules 7th congress of the World Association of Theoretical and Computational Chemists (WATOC08) Sydney, Australia, September 2008 (11.9MB)
  
• Visualization and modelling of exopolysaccharides from Inquilinus limosus Department of Life Sciences, University of Trieste, Trieste, Italy, June 2008 (16.5MB)