title: An Automated Force Field Topology Builder (ATB) and Repository: Version 1.0.
abstract: The Automated force field Topology Builder (ATB, http://compbio.biosci.uq.edu.au/atb ) is a Web-accessible server that can provide topologies and parameters for a wide range of molecules appropriate for use in molecular simulations, computational drug design, and X-ray refinement. The ATB has three primary functions: (1) to act as a repository for molecules that have been parametrized as part of the GROMOS family of force fields, (2) to act as a repository for pre-equilibrated systems for use as starting configurations in molecular dynamics simulations (solvent mixtures, lipid systems pre-equilibrated to adopt a specific phase, etc.), and (3) to generate force field descriptions of novel molecules compatible with the GROMOS family of force fields in a variety of formats (GROMOS, GROMACS, and CNS). Force field descriptions of novel molecules are derived using a multistep process in which results from quantum mechanical (QM) calculations are combined with a knowledge-based approach to ensure compatibility (as far as possible) with a specific parameter set of the GROMOS force field. The ATB has several unique features: (1) It requires that the user stipulate the protonation and tautomeric states of the molecule. (2) The symmetry of the molecule is analyzed to ensure that equivalent atoms are assigned identical parameters. (3) Charge groups are assigned automatically. (4) Where the assignment of a given parameter is ambiguous, a range of possible alternatives is provided. The ATB also provides several validation tools to assist the user to assess the degree to which the topology generated may be appropriate for a given task. In addition to detailing the steps involved in generating a force field topology compatible with a specific GROMOS parameter set (GROMOS 53A6), the challenges involved in the automatic generation of force field parameters for atomic simulations in general are discussed.
authors.affiliation: School of Chemistry and Molecular Biosciences, University of Queensland , St. Lucia, Australia.
authors.forename: Alpeshkumar K
authors.initials: AK
authors.lastname: Malde
authors.affiliation: School of Chemistry and Molecular Biosciences, University of Queensland , St. Lucia, Australia.
authors.forename: Le
authors.initials: L
authors.lastname: Zuo
authors.affiliation: School of Chemistry and Molecular Biosciences, University of Queensland , St. Lucia, Australia.
authors.forename: Matthew
authors.initials: M
authors.lastname: Breeze
authors.affiliation: School of Chemistry and Molecular Biosciences, University of Queensland , St. Lucia, Australia.
authors.forename: Martin
authors.initials: M
authors.lastname: Stroet
authors.affiliation: School of Chemistry and Molecular Biosciences, University of Queensland , St. Lucia, Australia.
authors.forename: David
authors.initials: D
authors.lastname: Poger
authors.affiliation: School of Chemistry and Molecular Biosciences, University of Queensland , St. Lucia, Australia.
authors.forename: Pramod C
authors.initials: PC
authors.lastname: Nair
authors.affiliation: Leiden/Amsterdam Center for Drug Research, Division of Molecular Toxicology, Vrije Universiteit Amsterdam , Amsterdam, The Netherlands.|Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences , Vienna, Austria.
authors.forename: Chris
authors.initials: C
authors.lastname: Oostenbrink
authors.affiliation: School of Chemistry and Molecular Biosciences, University of Queensland , St. Lucia, Australia.|Institute for Molecular Bioscience, University of Queensland , St. Lucia, QLD 4072, Australia.
authors.forename: Alan E
authors.initials: AE
authors.lastname: Mark