Data from simulations of mutations of tryptophan synthase

Data from the article "A Molecular Dynamics Simulation Study of the Effects of βGln114 Mutation on the DynamicBehavior of the Catalytic Site of the Tryptophan Synthase", A. Roy and M. Karttunen 

J. Chem. Inf. Model. (in press (2024)

Web: https://doi.org/10.1021/acs.jcim.3c01966

Preprint: https://doi.org/10.26434/chemrxiv-2023-4bhpv

Four systems of TS (Tryptophan Synthase):

   System = Denoted by

 E(PLP)  = e-plp

 E(AEX1) = e-aex1

 E(AA)   = e-aa

 E(c3)   = e-c3

Each system has 3 versions:

 wt     = WildType

 ala114 = mutated version (Gln114 mutated to Ala114)

 asn114 = mutated version (Gln114 mutated to Asn114)

Folder names:

     1_E(PLP) System Folders

 1_wt-e-plp

 2_ala114-e-plp

 3_asn114-e-plp

    2_E(AEX1) System Folders

 4_wt-e-aex1

 5_ala114-e-aex1

 6_asn114-e-aex1

    3_E(AA) System Folders

 7_wt-e-aa

 8_ala114-e-aa

 9_asn114-e-aa

    4_E(c3) System Folders

 10_wt-e-c3

 11_ala114-e-c3

 12_asn114-e-c3

File names:

Each folder contains AMBER readable topology, restart, input files, and also last frame pdb file:

initial system topology     = system.parm7

initial restart file               = system.rst7

minimization 1 input file   = min.in

minimization 1 restart file = min.rst7

minimization 2 input file    = min-all.in

minimization 2 restart file  = min-all.rst7

heating input file               = heat.in

heating restart file            = heat.rst7

equilibration input file       = equil.in

equilibration restart file     = equil.rst7

production 1 input file       = md.in

production 1 restart file     = md.rst7

production 2 input file       = md2.in

production 2 restart file     = md2.rst7

last frame of production    = frame40000_800ns.pdb