Pol1-DNA complex simulations

MD simulations of Pol1-DNA complex, started from the CC2 conformation (pdb 6RQL). Most missing loops were added with Maestro (2024-1) and the complex was shortly minimized using OPLS4 force field. The simulation system was prepared with Ambertools24. The complex was solvated with TIP3P water molecules with 12 Å buffer distance and the system was neutralized and physiological salt concentration of 0.15M was added using Na and Cl ions. MD simulations were conducted with Amber software using force fields ff19SB for the protein and OL21 for DNA. During the production runs the NPT ensemble was used: the 1.0 bar pressure was maintained with Monte Carlo barostat and 310 K temperature by Langevin thermostat. Frames were recorded every 0.2 ns and the total simulation time was 16*1000ns. The files were made ready for analysis by aligning and centering the complex, stripping away water molecules, Na and Cl ions, and writing the output in xtc format using cpptraj tool. The files include the 16 simulations in the xtc file (5,000 frames/simulation, total of 80,000 frames) and topology files as pdb and prmtop.