Automated Topology Builder
Automated Force Field Topology Builder (ATB) and Repository for the GROMOS family of force fields http://compbio.biosci.uq.edu.au/atb/
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:
* The study of biomolecule:ligand complexes * Free energy calculations * Structure-based drug design * The refinement of x-ray crystal complexes
This site provides:
* A repository for building blocks and interaction parameter files for molecules described using GROMOS force fields.
* An automated builder to help generate building blocks for novel molecules, compatible with the GROMOS 53A6 force field
and in formats appropriate for the GROMACS, GROMOS and CNS simulation packages.
* Refined geometries for molecules within the repository.
* Equilibrated starting coordinates for a range of biologically important systems.
Required Input:
* A coordinate file in Protein Data Bank (PDB) format (including all hydrogen atoms). * A connectivity record in PDB format listing all interatomic bonds. * The net charge on the molecule.
Output Provided:
* Building block files (all atom and united atom). * Interaction parameter files for the corresponding force field. * Optimized geometries (all atom and united atom).
The building block and interaction parameter files are provided in a range of formats that can be used to generate the appropriate topology files.
Disclaimer: While all effort has been made to provide appropriate estimates of the parameters including where appropriate alternative choices the user should carefully examine all files before use.
A detailed description of methodology used by the automated topology builder is given here. A detailed description of the software implementation is found here.
GROMOS home page is found here.
An introduction to the GROMOS force field is given here.
The compbio homepage is here.
