Parameters and protocol scripts for running CYP2D6 Molecular Dynamics Simulations
In this files you will find the scripts used to running MD in AMBER for protein CYP2D6/1*, MUT1 CYP2D6/Ser-488-Thr/Arg-329-Cys/Pro-487-Ser, and Mut2 CYP2D6/Ser-488-Thr/Glu-253-Lys/Pro-487-Ser/Deletion-Leu-209. We did not include trayectory files due to the limitation of space.
You will find all the requiered files to run the simulation, including heme parameters. If you want to conduct a simulation with different mutation, you can perfom such mutation using chimera and create a new parameter and topology files, using the tleap script (create_new_toppar.leap)