Supporting data for "Implicit electronic polarization via chargescaling in Amber OLx nucleic acid force fields improves ion pairing without backbone reparametrization"

Supporting data for the paper "Implicit electronic polarization via chargescaling in Amber OLx nucleic acid force fields improves ion pairing without backbone reparametrization" by J. Puyo-Fourtine, M. Zgarbova, L. Kantin, 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 Gromacs2 019.6 software, in 3 1-µs long replicates for each system and force field, at 300K, with an additional 10-µs 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.

Additionnally, we provide (in 5-othersystems.zip) the all-atom molecular dynamics simulations (1 µs) of varous DNA sequences: d(GAAGAGAAGC) (PDB ID 1AXP), d(GGGGCCCC)2, d(CGCA3 T3 GCG)2 (PDB ID 1S2R ), a Jun-Fos oligomer duplex d(GCATTCTGAGTCAG)  and a DNA/RNA hybrid r(GAAGAGAAGC)/d(GCTTCTCTTC) (PDB ID 1RRD)

Note: in the first verion of this upload, the OL15 simulations used by mistake the wrong type of KCl ions. This is now corrected.