Supporting data for "Amber-OL15-ECC: an Amber force field for nucleic acids with improved ion binding properties"

Supporting data for the paper "Amber-OL15-ECC: an Amber force field for nucleic acids with improved ion binding properties" by J. Puyo-Fourtine, M. Zgarbova, P. Jurecka and E. Duboué-Dijon.

This folder contains the all-atom molecular dynamics trajectories (without water) of the different systems analyzed in the associated paper, as follows: Dickerson-Drew dodecamer d(CGCGAATTCGCG)2 (PDB ID 1NAJ), the antiparallel guanine quadruplex (G-DNA) formed by the sequence d(G4T4G4 ) (PDB ID 2GWQ, chain A) , a left-handed Z-DNA hexamer duplex d(CGCGCG)2 (PDB ID 1ICK 91, not including spermine and Mg2+ ions)  and a double stranded A-RNA decamer r(GCACCGUUGG)2 (1QC0’ excised from PDB 1QC0). The nucleic acid sequences are explicitly solvated and neutralized with KCl, with an additional 150mM KCl background electrolyte (2M for Z-DNA).
Simulations for each systems are provided with both the Amber-OL15 and Amber-OL15-ECC force fields (as well as with Amber-OL21 and Amber-OL21-ECC for Z-DNA and G-DNA), combined with the SPC/E force field for water. Simulations have been performed using the Gromacs2019.6 software, in 3 1-us long replicates for each system and force field, at 300K, with an additional 10-us simulation for the G-DNA and Z-DNA systems.

In each folder, in addition to the trajectory (without water molecules) and structure file, we provide the employed topology (.top and .itp) and input (.mdp) files. We also provide the CPPTRAJ scripts to analyze conformational properties, as well as the raw output of this analysis for each system. The ionmaps folder contains for each system and force field the computed K+ density maps.