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Web Name: ATB | Home

WebSite: http://atb.uq.edu.au

ID:207243

Keywords:

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Description:

keywords:ATB, automated, auto, automatic, automatic topology builder, topology, builder, repository, molecules, molecular dynamics, MD, gromacs, gromos, 54a7, forcefield, force field, bond, angle, dihedral, improper dihedral, coulomb, Lennard-Jones, LAMMPS, CNS, NMR, CIF, PDB, ligand, drug
description:The Automated Topology Builder (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 and refinement of x-ray crystal complexes.
Automated Topology Builder (ATB) and Repository
Version 3.0 Home ATB version 3.0

Improved agreement with experimental solvation data.

Recently processed Formula C₁₇H₁₆N₂O₄ Number of atoms 39 Net Charge 0 Click to toggle size.">

Superposition of QM optimised (green) and MM energy minimised (cyan) structures.
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Site statistics Pre-calculated molecules 574,266 Registered users 15,752 Downloads per month 5,800 Overview

The ATB provides classical molecular force fields for novel compounds. Applications include:

The study of biomolecule:ligand complexes Structure-based drug design Material engineering The refinement of x-ray crystal complexes

This site provides: Access to classical force fields in formats compatible with GROMACS, GROMOS and LAMMPS simulation packages and CNS, Phenix, CCP4, Refmac5 and CYANA X-ray and NMR refinement packages. A GROMOS to AMBER topology file converter. Optimised geometries for molecules within the repository.

ATB3.0 key features User interface Submission of molecules with molecular drawer, SMILES or PDB file. Search a database of pre-calculated molecules with various descriptors including 3D structures. Links to molecules in other databases including ChEMBL, RCSB PDB, and ChemSpider. Save molecules of interest. 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. A tool to match and reorder PDB files for identical molecules with alternative atom names and/or atom order: PDB Match and Reorder. Parameter generation Lennard Jones parameters refined against experimental solvation and pure liquid properties. ATB parametrisation and validation is performed using a single-range 1.4 nm cutoff for both Lennard Jones and Coulomb interactions (see FAQ). Atomic charges fitted to QM electrostatic potentials at B3LYP/6-31G* level of theory (for molecules < 50 atoms). Robust symmetry routines to ensure identical parameters are assigned to chemically equivalent atoms, bonds and angles. Bonded parameter assignment using force constants estimated from Hessian (B3LYP/6-31G*, for molecules < 40 atoms). Automated calculation pipeline Automated QM calculation pipeline with error recovery (low failure rate). Automated QM and MM energy minimised structure comparison. Automated calculation of solvation free energies (restricted). Output formats GROMACS (GROMOS 54A7). GROMOS96 (GROMOS 54A7). GROMOS11 (GROMOS 54A7). LAMMPS (GROMOS 54A7). APBS (Adaptive Poisson-Boltzmann Solver) file format (.pqr). CNS (Crystallography NMR System). CCD CIF (compatible with the Phenix, CCP4, Refmac5 and CYANA X-ray and NMR refinement packages). eLBOW CIF (compatible with the Phenix X-ray refinement packages). An extended and generalized mmCIF format incorporating a complete description of all force field parameters including units. AMBER via a tool to convert GROMOS system topology files (.top) to the AMBER format (.prmtop). Publications

Description

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.
J. Chem. Theory Comput., 2011, 7, 4026-4037. DOI:10.1021/ct200196m

Validation

Stroet M, Caron B, Visscher K, Geerke D, Malde AK, Mark AE.
Automated Topology Builder version 3.0: Prediction of solvation free enthalpies in water and hexane.
DOI:10.1021/acs.jctc.8b00768

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.
J. Comput. Aided. Mol. Des., 2014, 28, 221-233. DOI:10.1007/s10822-014-9713-7

Related work

van Gunsteren WF, Daura X, Fuchs PFJ, Hansen N, Horta BAC, Hunenberger PH, Mark AE, Pechlaner M, Riniker S, Oostenbrink C
On the effect of the various assumptions and approximations used in molecular simulations on the properties of bio-molecular systems: Overview and perspective on issues
ChemPhysChem 2021, 22, 264-282. DOI:10.1002/cphc.202000968

Stroet M, Koziara KB, Malde AK, Mark AE.
Optimization of empirical force fields by parameter space mapping: A single-step perturbation approach.
J. Chem. Theory Comput., 2017, 13, 6201-6212. DOI:10.1021/acs.jctc.7b00800

Reisser S, Poger D, Stroet M, Mark AE.
Real cost of speed: The effect of a time-saving multiple-time-stepping algorithm on the accuracy of molecular dynamics simulations.
J. Chem. Theory Comput., 2017, 13, 2367-2372. DOI:10.1021/acs.jctc.7b00178

Malde AK, Stroet M, Caron B, Visscher K, Mark AE.
Predicting the prevalence of alternative warfarin tautomers in solution.
J. Chem. Theory Comput., 2018, 14, 4405-4415. DOI:10.1021/acs.jctc.8b00453

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.
J. Comput. Biol., 2013, 20, 188-198. DOI:10.1089/cmb.2012.0239

Engler MS, Caron B, Veen L, Geerke DP, Mark AE, Klau GW.
Multiple-choice knapsack for assigning partial atomic charges in drug-like molecules.
LIPIcs-Leibniz International Proceedings in Informatics 113, 2018, DOI:10.4230/LIPIcs.WABI.2018.16

Schmid N, Eichenberger AP, Choutko A, Riniker S, Winger M, Mark AE and van Gunsteren WF.
Definition and testing of the GROMOS force-field versions 54A7 and 54B7.
Eur. Biophys. J., 2011, 40, 843-856. DOI:10.1007/s00249-011-0700-9

Oostenbrink C, Villa A, Mark AE and van Gunsteren WF.
A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6.
J. Comput. Chem. 2004, 25, 1656-1676. DOI:10.1002/jcc.20090

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. Start by Browsing Existing Molecules Contact

For queries regarding the ATB, please contact:

UQ MD Group Website

Contributors Scientific Development: Alan E. Mark Martin Stroet Alpesh K. Malde
This project is supported by the Australian Research Data Commons (ARDC). The ARDC is enabled by NCRIS.

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The Automated Topology Builder (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 and refinement of x-ray crystal complexes.

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