Automated Topology Builder

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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.

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