You need to split that code into two parts.
[T,Y] = ode15s(@vdp1000,[0 3000],[2 0]);
plot(T,Y(:,1),'-o')
should be in one file, and
function dy = vdp1000(t,y)
dy = zeros(2,1);
dy(1) = y(2);
dy(2) = 1000*(1 - y(1)^2)*y(2) - y(1);
should be in vdp1000.
You would invoke the other file, not the vdp1000 file.
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