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Nat Methods. 2016 Jan;13(1):55-8. doi: 10.1038/nmeth.3658. Epub 2015 Nov 16.

Parmbsc1: a refined force field for DNA simulations.

Author information

1
Institute for Research in Biomedicine (IRB) Barcelona, the Barcelona Institute of Science and Technology, Barcelona, Spain.
2
Joint BSC-IRB Research Program in Computational Biology, IRB Barcelona, Barcelona, Spain.
3
School of Physics and Astronomy, University of Leeds, Leeds, UK.
4
Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, USA.
5
Barcelona Supercomputing Center, Barcelona, Spain.
6
Department of Chemistry, University of Cambridge, Cambridge, UK.
7
Department of Biochemistry and Molecular Biology, University of Barcelona, Barcelona, Spain.
8
Instituto de Química Física 'Rocasolano', Consejo Superior de Investigaciones Cientificas, Madrid, Spain.
9
School of Pharmacy, University of Nottingham, Nottingham, UK.
10
Centre for Biomolecular Sciences, University of Nottingham, Nottingham, UK.
11
Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, USA.

Abstract

We present parmbsc1, a force field for DNA atomistic simulation, which has been parameterized from high-level quantum mechanical data and tested for nearly 100 systems (representing a total simulation time of ∼ 140 μs) covering most of DNA structural space. Parmbsc1 provides high-quality results in diverse systems. Parameters and trajectories are available at http://mmb.irbbarcelona.org/ParmBSC1/.

PMID:
26569599
PMCID:
PMC4700514
DOI:
10.1038/nmeth.3658
[Indexed for MEDLINE]
Free PMC Article

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