MD and EVB parameters for the manuscript titled: Sequence – Dynamics – Function Relationships in Protein Tyrosine Phosphatases

This repo is split into the following subfolders: ######### MD_Simulations: ######### The starting structures used to perform all MD simulations in our paper. Alongside the input files used to run the MD simulations. 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 phosphoenzyme intermediate residue are provided alongside an example tleap script that was used to prepare each structure. Please see the paper for details on how each structure was prepared. The input files have the following order of operations: 1. minsolv.in 2. mdsolv.in 3. min.in 4. heat.in 5. npt1.in 6. npt2.in 7. npt3.in 8. npt4.in 9. eqnpt.in 10. prod_100ns.in (repeated 5x to make 500 ns). For the starting structures, each file is named according to how it was produced. For example: YopH_Chi2_6DR7_CSP_Bound - Chimera 2 built using the PDB 6DR7. YopH_Chi2_WT_Closed_Start - Chimera 2 built using the WT closed conformation. ######### Steered_MD_Simulations: ######### Input files used to run the steered/targeted MD simulations described in our paper. Each structure used was first equilibrated using the same protocol as in our standard MD simulations. Plumed was used in combination with Amber to run the steered MD simulations. The plumed file used alongside the required structure files for the steered MD simulations are provided. Please see the paper for a description of the steered MD protocol used. ######### EVB_Simulations ######### EVB simulations were performed using Q6. We have previously simulated both WT YopH and WT PTP1B, so those inputs are not described here. The order of operations for the equil files is as follows: "dyn_min_wat_noshake", "dyn_min_wat", "dyn_min_wat_eq", "dyn_cool", "dyn_min", "dyn_warm30k", "dyn_warm150k", "dyn_warm300k", "dyn_eq300k_{1..20}". With 30 replicas performed per complex. The production runs were performed inside each equilibration run folder inside a folder called "2.evb