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Overview

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 simulation packages and CNS, Phenix, CCP4 and Refmac5 X-ray refinement packages.
  • Refined geometries for molecules within the repository.
  • Equilibrated starting coordinates for a range of biologically important systems.

Version 2.2 Change Log

Redesigned user interface

  • Graphical and SMILES string molecule submission.
  • Structure based searching of existing molecular database.
  • Automated generation of common and IUPAC names and links to the ChemSpider database.
  • Prediction of 1H NMR spectra.
  • Ability to import molecules into a private database.
  • Provision of an API for automated access to the database (on request).
  • Tools to visualize and compare parameters for molecules submitted in alternative conformations and for users to flag problems with specific molecules.

Enhanced parameter assignment

  • Improved atom ordering.
  • Robust symmetry routines to ensure identical parameters are assigned to chemically equivalent atoms, angles and bonds.
  • Improved bonded parameter and exclusion assignment for molecules with internal stress.
  • Refined/new halogen atom parameters (Cl, Br and I).
  • Parameters for additional atom types (e.g. Se and B).

Expanded pipeline capability

  • Improved stability.
  • Automated calculation of solvation free energies (restricted).
  • Automated selection of QM methodology and error recovery (low failure rate).
  • Automated energy minimization and validation.

Expanded range of formats

  • GROMACS (gromos 53A6 and 54A7).
  • GROMOS96 (gromos 53A6 and 54A7).
  • GROMOS11(gromos 53A6 and 54A7).
  • APBS (Adaptive Poisson-Boltzmann Solver) file format (.pqr).
  • CNS (Crystallography & NMR System).
  • CIF (compatible with the Phenix, CCP4 and Refmac5 X-ray refinement packages).
  • An extended and generalized mmCIF format incorporating a complete description of all force field parameters including units.

News and References

Recent Changes

  • Version 2.2 includes: improvements in the consistency of the parameters, and a full redesign of the user interface.
  • Version 2.1 updates include: greater stability of the pipeline, improved atom ordering, improved symmetry and minor changes to bonded parameter assignment.

ATB 2.0 Validation Study

  • Koziara KB, Stroet M, Malde AK, Mark AE.
    Testing and validation of the Automated Topology Builder (ATB) version 2.0: prediction of hydration free enthalpies.
    Journal of Computer-Aided Molecular Design, 2014.
    DOI:10.1007/s10822-014-9713-7

Improved Charge Group Assignment used for 2.0 topologies

  • Canzar S, El-Kebir M, Pool R, Elbassioni K, Malde AK, Mark AE, Geerke DP, Stougie L, Klau GW.
    Charge Group Partitioning in Biomolecular Simulation.
    Journal of Computational Biology, 2013, 20, 188-198.
    DOI:10.1089/cmb.2012.0239

ATB Original Paper

  • Malde AK, Zuo L, Breeze M, Stroet M, Poger D, Nair PC, Oostenbrink C, Mark AE.
    An Automated force field Topology Builder (ATB) and repository: version 1.0.
    Journal of Chemical Theory and Computation, 2011, 7(12), 4026-4037.
    DOI: 10.1021/ct200196m

Latest ATB forcefield files

GROMOS 54A7 IFP files with additions from the ATB:

GROMOS 53A6 IFP files with additions from the ATB:

Conditions of Use

The Automated Topology Builder (ATB) and Repository has been developed and is currently maintained with support from the University of Queensland (UQ), the Australian Research Council (ARC) and the Queensland Cyber Infrastructure Foundation (QCIF). Access to the ATB is provided free to academic users from publically funded teaching or research institutions. Access for academic use is conditional on: i) any molecule submitted to the ATB being made publically available and ii) the source of any material downloaded from the ATB being appropriately acknowledged in any publications or other forms in which research using this material is disseminated.

Use of the ATB by other parties, or academic users wishing to restrict the access of others to specific molecules, is considered to be commercial in nature. Commercial access is available by licence or collaborative agreement. Parties interested in commercial licencing or other arrangements should contact Prof Alan E. Mark at the address provided at the bottom of the page.

Getting started

See the FAQ page to get started.

Tutorials for common tasks on the ATB are currently being developed, the first of which is available here: How to View an Existing Molecule

Disclaimer

While every effort has been made to provide reliable estimates of the parameters including where appropriate alternative choices of parameters, these are intended as a guide. The user should carefully examine all files before use and the suitability of the parameters provided for any specific application cannot be guaranteed.