Mechanism for Nucleotidyl Transfer in LINE-1 ORF2p Revealed by QM/MM Simulations

The entire QM/MM model utilized to perform QM/MM MD simulations of the reverse transcriptase activity in LINE-1 ORF2p Revealed by QM/MM (qmmm_model.pdb and qmmm_model.psf). PSF file for the QM part (qm.psf) Trajectory files in the dcd format of the biased QM/MM MD umbrella sampling simulations and unconstrained simulations of the ES complex. Corresponding values a reaction coordinate at each MD frame are in text files in the trajs.zip archive.