Do you have the Global Optimization Toolbox? That's the first step if you want to use GA.
See this on how to set your problem up: http://www.mathworks.com/help/gads/index.html#optimization-problem-setup
Try writing your objective as something like this:
function objectiveVal = myFunction(x)
a = x(1);
b = x(2);
c = x(3);
d = x(4);
e = x(5);
% Call your other software
objectiveVal = otherSoftwareCall(a,b,c,d,e);
