If you let dx/dt = vx, say, and dy/dt = vy, then the accelerations can be written as dvx/dt = -gamma/m*vx*sqrt(vx^2+vy^2), and dvy/dt = -g-...etc. You write a function that calculates the velocities and accelerations at an instant of time, and then returns them as a column vector to ode45. ode45 must call this function with a timespan and a vector with initial values for x, y, vx and vy.
doc ode45
for more detail.
