Input files for "Energetics of Expanded PAM Readability by Engineered Cas9-NG"

Input files, topologies, coordinates, harmonic restraints and simulation control files for “Energetics of Expanded PAM Readability by Engineered Cas9-NG”

Details for compressed directory "Hybrid_topologies_coordinates_structure_And_Restraint_files"

The directory, "Hybrid_topologies_coordinates_structure_And_Restraint_files" contains sub-directories corresponding to the name of the residues mutated in the alchemical simulation (R1335V, E1219F, D1135V, L1111R, T1337R, T1337R_in_SpCas9R2V,E2F, G1218R, A1322R, All_Mutations).

Within individual mutation directories, five sub-directories are present, which represent five different systems (four complexes with TGG, TGA, TGT, TGC PAM containing, and one free DNA unbound state) for individual mutations.

These sub-directories contain input files, coordinate files, restraint files, scripts, topologies, and structure files for individual systems used for conventional/alchemical simulations (refer to Table S1). 

Details for compressed directory "MD_and_FEP_run_scripts"

This directory contains ten subdirectories:

Directories "Minimize" and "Heating" contain NAMD scripts for energy minimization and slow heating to the desired temperature. 

Directories "Eq1, Eq2, Eq3, Eq4" contain NAMD script files for running equilibration at different harmonic restraint conditions. 

Directory "MD" contains the NAMD script file for running 200 ns production dynamics.

Directory "FEP_5ns" contains NAMD script (5ns.namd) for running Free Energy Perturbation (FEP) alchemical simulation of the mutation of interest by using 51 equally spaced λ points from λ=0 to λ=1, with each λ window simulated for 5 ns. 

Directory "tools contain tcl" script file used by 5ns.namd to run Free Energy Perturbation (FEP). 

Directory "toppar" contains topology files and force field parameters for the CHARMM36 force field.