This repo is split into the following subfolders:

######### Classical_MD_Simulations: #########
The starting structures used to perform all MD simulations in our paper are collected at Starting_Structures folder: 
        * Des27_unliganded.pdb
        * Des27_liganded.pdb
        * Des27.7_unliganded.pdb
        * Des27.7_liganded.pdb

Alongside the input files used for the equilibration and production of the MD simulations are at Inputs_MD folder. Simulations were performed with Amber and the final step used to prepare each structure was with tleap (part of amber tools).

The parameters for the substrate (5-nitrobenzioxazole) are at Parameter_SUB folder. 

Please see the paper for details on how each structure was prepared. 


######### EVB_Simulations ######### 
The files required for the MD level minimization with Amber22 are in the 1_Amber_minimization folder:
    The starting structures are in the 0_starting_structures folder:
        * Des27_WT_IN.pdb
        * Des27_WT_OUT.pdb
        * Des27_7_IN.pdb
        * Des27_7_OUT.pdb
The input files required to carry out the minimization are in the 1_minimization folder.
EVB simulations were performed using Q6, with 30 replicas performed per complex. The required files are in the 2_Q6_simulation folder
The Amber22 minimized starting structures are in the 0_starting_structures folder, including the pdb, topology and fep files prepared for Q6, following the same naming.
The generalized input files required for Q6 equilibration are in the 1_Q6_equilibration folder
The EVB simulation input files for Q6 are in the 2_Q6_EVB folder