Abstract
Here are the pdb files for the simulations with only 6 central SNAREs and 6 central and 6 peripheral SNAREs with C2B of Syt1 and residue 51-75 of Cpx1 shown in figure 3.
File for figure 3a: ic_6c_snares.pdb is the initial condition for simulations with only 6 central SNAREs, and the tcl file figure_3a.tcl is to show this initial condition.
File for figure 3b: ic_6c6p_snares_c2b.pdb is the initial condition for simulations with 6 central and 6 peripheral SNAREs with a vesicle, and the tcl file figure_3b_top_view.tcl and figure_3b_side_view.tcl are to show this initial condition.
File for figure 3c: ic_6c6p_snares_c2b_nd.pdb is the initial condition for simulations with 6 central and 6 peripheral SNAREs with a nanodisc and ic_6c6p_snares_c2b_nd.xtc file is the corresponding trajectory of this simulation. The tcl file movie_for_figure_3c.tcl is to show the movie of this simulation. If you want to look at all proteins in this simulation, the tcl file movie_for_figure_3c_all.tcl can do that.
To view these snapshots by VMD, load the corresponding .tcl file or run "vmd -e name.tcl" in your terminal.