An automated force field topology builder (ATB) and repository: Version 1.0

Malde, Alpeshkumar K., Zuo, Le, Breeze, Matthew, Stroet, Martin, Poger, David, Nair, Pramod C., Oostenbrink, Chris and Mark, Alan E. (2011) An automated force field topology builder (ATB) and repository: Version 1.0. Journal of Chemical Theory and Computation, 7 12: 4026-4037.


Author Malde, Alpeshkumar K.
Zuo, Le
Breeze, Matthew
Stroet, Martin
Poger, David
Nair, Pramod C.
Oostenbrink, Chris
Mark, Alan E.
Title An automated force field topology builder (ATB) and repository: Version 1.0
Journal name Journal of Chemical Theory and Computation   Check publisher's open access policy
ISSN 1549-9618
1549-9626
Publication date 2011-12-13
Sub-type Article (original research)
DOI 10.1021/ct200196m
Volume 7
Issue 12
Start page 4026
End page 4037
Total pages 12
Place of publication Washington, DC, United States
Publisher American Chemical Society
Collection year 2012
Language eng
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.
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ
Additional Notes Published online 27 October 2011

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2012 Collection
School of Chemistry and Molecular Biosciences
 
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Created: Mon, 14 Nov 2011, 22:19:55 EST by Dr Alpeshkumar Malde on behalf of School of Chemistry & Molecular Biosciences