Molecular Dynamics simulations of different G-quadruplexes folding in presence of dimeric N-methylbenzo[c]acridinium derivatives

Molecular Dynamics simulations of different G-quadruplexes folding in presence of dimeric N-methylbenzo[c]acridinium derivatives. Two derivatives are considered, called 2 and 2prim. For G-quadruplexes structures are considered: parallel (PDB code 2MGN), hybrid1 (PDB code 2HY9), hybrid2 (PDB code 2JPZ), anti-parallel chair conformation (PDB 9JX5). We provide force field parameters file for the two derivative (lib, mol2 and frcmod files). Two sets of simulations have been run: first set in a 4:1 stoichiometry starting with 2 and 2prim in solvent (1 frame every 100 ps, 5x200 ns) second set in a 2:1 stoichiometry starting with 2 and 2prim bound to G-quadruplexes (1 frame every 1 ns, 400 ns). "nok" means no potassium ions is present in the structures In additions, we provide: the simulations of the two hybrides structures without potassium cations (hybrid1/2_nok.nc, 1 frame every 1 ns, 400ns). the simulation of 4:1 stoichiometry with dsDNA CG rich sequence (1 frame every 100 ps, 5x200 ns)