The ATB and Repository is intended to facilitate the development of molecular force fields for Molecular Dynamics or Monte Carlo simulations of biomolecular systems. Applications include:
This site provides:
The building block and interaction parameter files are provided in a range of formats that can be used to generate the appropriate topology files.
The topology builder uses a knowledge-based approach in combination with QM calculations to select parameters consistent with a given force field.
The molecule is initially optimised at the HF/STO-3G (or AM1 or PM3) level then re-optimised at the B3LYP/6-31G* level of theory in implicit solvent (water). The initial charges are estimated by fitting the electrostatic potential using Kollmann-Singh scheme. The Hessian matrix is calculated.
The topology is constructed as follows:
We would like to acknowledge the many people who have provided feedback during the development phase of this project, in particular, Wilfred van Gunsteren, Philippe Hünenberger, Volker Knecht, Alexandre Bonvin, Bruno Horta, Samuel Genheden and MD group at The University of Queensland, Australia
We would also like to thank Peter Ertl for providing us with the JSME molecular builder.
Software and tools:
GROMOS Lipid Forcefields:
GROMOS Sugar Forcefields: