Parmbsc1: a refined force field for DNA simulations

Ivani, Ivan; Dans, Pablo D.; Noy, Agnes; P�rez, Alberto; Faustino, Ignacio; Hospital, Adam; Walther, J�rgen; Andrio, Pau; Go�i, Ramon; Balaceanu, Alexandra; Portella, Guillem; Battistini, Federica; Lluis Gelp�, Josep; Gonz�lez, Carlos; Vendruscolo, Michele; Harris, Sarah A.; Laughton, Charles A.; Case, David A; Orozco, Modesto

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 ?s) 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/.

Citation

Ivani, I., Dans, P. D., Noy, A., Pérez, A., Faustino, I., Hospital, A., …Orozco, M. (2016). Parmbsc1: a refined force field for DNA simulations. Nature Methods, 13(1), 55-61. https://doi.org/10.1038/NMETH.3658

• Journal Article Type: Article
• Acceptance Date: Sep 22, 2015
• Online Publication Date: Nov 16, 2015
• Publication Date: Jan 15, 2016
• Deposit Date: Dec 20, 2017
• Print ISSN: 1548-7091
• Publisher: Nature Publishing Group
• Peer Reviewed: Peer Reviewed
• Volume: 13
• Issue: 1
• Pages: 55-61
• DOI: https://doi.org/10.1038/NMETH.3658
• Public URL: https://nottingham-repository.worktribe.com/output/1110241
• Publisher URL: https://www.nature.com/articles/nmeth.3658