Molecular dynamics simulations of PCBP1 protein and DNA i-motif

Amber topology (.prmtop) and trajectory files (.pdb) of PCBP1 protein with i-motif. Water and ions where stripped, frames are saved every 1 ns. Five structures where generated using RosettaFoldDNA, the protein structures coming from previous MD simulations of RosettaFold (struct1-3) or alphafold (struct 4-5) models. Three protonation states of cytosines of i-motif are considered: none of cytosine is positively charged (seta) half of the cytosine pairs contain a positively charged cytosine (setb) all of the cytosine pairs contain a positively charged cytosine (setc)