Carbohydrate Force Fields

For a full description of the force fields and how to load them, please read Chapter 3 of the Amber Reference Manual.

GLYCAM-06j

GLYCAM parameters for carbohydrates are maintained by the group of Robert J. Woods at the Complex Carbohydrate Research Center at the University of Georgia in Athens GA. Versioning, file sanity, and online access are maintained primarly by B. Lachele Foley.

The most recent GLYCAM force field is the GLYCAM-06j parameter set. To ensure compatibility with Amber parameter sets for other biomolecules, a variation on the GLYCAM atom types have been introduced.

Ref: K. N. Kirschner; A. B. Yongye; S. M. Tschampel; J. González-Outeiriño; C. R. Daniels; B. L. Foley; R. J. Woods. GLYCAM06: A generalizable biomolecular force field. Carbohydrates. J. Comput. Chem., 2008, 29, 622–655.

GLYCAM Resources

Tools for simplifying the generation of structure and topology files for performing simulations of oligosaccharides, glycoconjugates and glycoproteins are also available on the GLYCAM website (glycam.org).

GLYCAM-Web has been integrated into several glycomics databases, such as the Consortium for Functional Glycomics (functionalglycomics.org).

Getting Help

If you need general help with using the GLYCAM force fields in AMBER, please use the AMBER Mailing List. Many questions are already answered in the archives. If you need help with tasks specific to carbohydrates, and you do not find the answer on the AMBER Mailing List, try the GLYCAM users mailing list.

Legacy Utilities of Interest

The Amber/Glycam Input Configurator, a web-based interface to help prepare inputs for simulations with the carbohydrate force fields is also available. This feature is not updated with each new version of Amber. However, the settings and protocols it suggests are a way to get started.