So your equation is not a PDE, but a simple ODE.
Either you try to artificially set du/dx = 0 at both ends and see whether the results make sense.
Or you use Bill Greene's code who claims that ODEs can be handled therein.
Or - as you wrote that there is another problem with your equations that pdepe cannot handle (sigmoid function) - discretize your equations in space and use ODE15S to solve the resulting system of ordinary differential equations in the grid points. Look up "method-of-lines" for more details.