EVB Parameters for the Manuscript: Complex Loop Dynamics Underpin Activity, Specificity and Evolvability in the (Beta-Alpha)8 Barrel Enzymes of Histidine and Tryptophan Biosynthesis

Starting structures, topologies, input + parameter files for the empirical valence bond (EVB) simulations performed to generate the data for the article: Complex Loop Dynamics Underpin Activity, Specificity and Evolvability in the (beta-alpha)8 Barrel Enzymes of Histidine and Tryptophan Biosynthesis (in submission). Documentation (Same as in the README.txt file): In this folder, you will find all the items you need to reproduce our EVB simulations. You should first be familiar with the EVB method, a good starting point for this can be found here: https://onlinelibrary.wiley.com/doi/book/10.1002/9781119245544 Each subfolder contains example input files needed to run the EVB equil and production simulations for a given system. Further, a folder with all the coordinate files (Starting PDBs), as well as a folder with all the topology files (Topopogies) used along this work are provided. All the required libraries and parameter files required to build the systems are provided in the folder "libs", together with the fep files for both ProFAR and PRA ring opening step reactions. ### 1. Equilibration part. Example input files for the equilibration are attached alongside all the topologies and coordinate files. Note that for each replica you need to choose a new random seed (defined in: "1-dyn_min_wat_noshake_verysmall") The order of operations for the equil files is as follows: "1-dyn_min_wat_noshake_verysmall" "2-dyn_min_wat_noshake_bitsmall" "3-dyn_min_wat_noshake_small" "4-dyn_min_wat_noshake" "5-dyn_min_wat" "6-dyn_min_wat_eq" "7-dyn_cool" "8-dyn_min" "9-dyn_warm150k" "10-dyn_warmRT" "11-dyn_eqRT" "12-dyn_eqPUB" "13-dyn_eqPUB" "14-dyn_eqPUB" "15-dyn_eqPUB" ### 2. Production part. The production runs were performed inside each equilibration run folder. The order of the operations for the production files is sequentially. "fep_000_*.inp", "fep_001_*.inp" "fep_{003..050}*.inp". Note that the files PRA.fep and ProFAR.fep in the "lib" folder contain the parameters describing the EVB atoms in our simulation