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., Walther, J., Andrio, P., Goñi, R., Balaceanu, A., Portella, G., Battistini, F., Lluis Gelpí, J., González, C., Vendruscolo, M., Harris, S. A., Laughton, C. A., Case, D. 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