Software for building 3D molecular structures of carbohydrates.
This application was developed using C# under .Net framework. It can be run from Linux and Windows.
- CarbBuilder: an adjustable tool for building 3D molecular structures of carbohydrates for molecular simulation M. Kuttel, Y. Mao, M. Lundborg and G. Widmalm Proceedings of 7th IEEE International Conference on e-Science , 5-8 December 2011, Stockholm, Sweden (paper accepted)
- Carbohydrate Solution Force Field (CSFF)
- 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:
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)