Available downloads

Publicly available code and data can be accessed on GitHub and Bitbucket. 

BRIDGE

Biomolecular Reaction and Interaction Dynamics Global Environment (BRIDGE) can be used to set up and simulate biological macromolecules, perform conformational analysis from trajectory data and conduct data analytics of large scale protein motions using statistical rigor.Enzyme reaction dynamics and drug design package

Classical Parameters

  • The Carbohydrate Solution Force Field (CSFF)

    M. Kuttel and J. W. Brady and K. J. Naidoo. “Carbohydrate Solution Simulations: Producing a Force Field with Experimentally Consistent Primary Alcohol Rotational Frequencies and Populations”, J. Comput. Chem. 2002, 23, 1236-1243.

  • The Metal Solution Force Field (MSFF)

    Richard P. Matthews and Kevin J. Naidoo. “Experimentally Consistent Ion Association Predicted for Metal Solutions from Free Energy Simulations”, J. Phys. Chem. B. 2010, 114(21), 7286-7293.

  • CHARMM Ferriheme Force Field

    D. Kuter, V Streltzov, N Davydova, GA Venter, KJ Naidoo and TJ Egan. “Molecular Structures and Solvation of Free Monomeric and Dimeric Ferriheme in Aqueous Solution: Insights from Molecular Dynamics Simulations and Extended X-ray Absorption Fine Structure Spectroscopy”, Inorg. Chem., 2014 Oct.

Quantum Parameters

SCRU has parameterised semi-empirical quantum force fields in order to improve their behaviour for chemical glycobiology. These new parameter sets are called AM1d-CB1, AM1*-CB1