An Automated Force Field Topology Builder (ATB) and Repository: Version 1.0.

By Alpeshkumar K. Malde, Le Zuo, M. Breeze, Martin Stroet, David Poger, Pramod C. Nair, Chris Oostenbrink, Alan E. Mark. Journal of Chemical Theory and Computation, 2011

1,716 citations recorded by the source corpus.

Subfields: Atomic and Molecular Physics, and Optics, Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/1e02864838f6e9c25afc0f02a9a37a5ac3adb2a3

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In Atomic and Molecular Physics, and Optics

1. Justin A. Lemkul
2. David L. Mobley
3. D. van der Spoel
4. J. Guthrie
5. Erik Lindahl
6. Michael R. Shirts
7. Wim F. Vranken
8. A. W. Sousa da Silva

In Materials Chemistry

1. Justin A. Lemkul
2. A. W. Sousa da Silva
3. Wim F. Vranken
4. João P. G. L. M. Rodrigues
5. Michael R. Shirts
6. Ezgi Karaca
7. D. van der Spoel
8. Szilárd Páll

In Molecular Biology

1. Justin A. Lemkul
2. David L. Mobley
3. João P. G. L. M. Rodrigues
4. Alexandre M. J. J. Bonvin
5. Ezgi Karaca
6. J. Guthrie
7. Wim F. Vranken
8. A. W. Sousa da Silva

Citations in the corpus

• From Proteins to Perturbed Hamiltonians: A Suite of Tutorials for the GROMACS-2018 Molecular Simulation Package [Article v1.0] (2019, methodology): “A simple method to obtain both coordinates and topology for use with GROMOS force fields are online servers PRODRG [64] and ATB [65].”
• Testing and validation of the Automated Topology Builder (ATB) version 2.0: prediction of hydration free enthalpies (2014, neutral): “au/atb/) and Repository [18] has been developed to provide interaction parameters for a wide range of molecules compatible with the GROMOS force field [19].”
• ACPYPE - AnteChamber PYthon Parser interfacE (2012, methodology): “Finally, the recently developed Automated Topology Builder (ATB) [14] is limited in scope because it only generates topologies compatible with the GROMOS 53A6 [15] force field.”
• GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit (2013, background): “Constraints such as those used in refinement can be applied either to positions, atomic distances, or torsions, and there are several options for ensemble weighting of contributions from multiple constraints.”
• Information-driven structural modelling of protein-protein interactions. (2015, methodology): “For those molecules not in the list, the user is left to generate their own parameterization scheme, using for example PRODRG [41], ACPYPE [42], or ATB [43], and provide the necessary files (topology and parameters in CNS format) in the toppar/ directory: ligand.top and ligand.par .”
• Blind prediction of solvation free energies from the SAMPL4 challenge (2014, methodology): “Submission 529 used MD alchemical free energy calculations in explicit solvent with the GROMOS simulation package, using parameters from Automated Topology Builder [21, 22].”