Minimalizing two variables back to back

So i have two variables, P1 and P2 that i am trying to optimise by minimalising a function.

clear
V1 = fminsearch(@SepScoreMatch,17); %function to optimise a value of V1
V2 = fminsearch(@SepScoreMatchP2,0.1); %function to optimise a value of V2 using the value of V1.

However, when i try to run this i get the error 'Unrecognized function or variable 'V1'.'

Is there a way i can write this for it to work? Possibly putting V1 = fm..... as the first line of V2?

Also is there a 'better' was i could do this. For instance is there a minimalising function that optimises one parameter then the other?

The function for V1 is basically matching the x values of the max points (the graph looks like a 'u' in shape so has two peaks) of a curve in a graph and V2 is basically the width which i do by

score = 1:length(ygraph2);

for i = 1:length(y2)
    diffsquared = (y1(i,1)-y2(i,1))^2;
    score(i) = diffsquared;
end

MeanScore = mean(score);

Sadly i cant just fmin both variables at the same time as graph 2 is always much wider than graph 1. So it tries to minimalise Meanscore by making the tips of the graph wider a which leads to an overeall smaller value of

TotalScore = PeakDiff+MeanScore

but less accurate actual values. This is why i am trying to optimise one then the other.

[Walter Roberson]

See http://www.mathworks.com/help/matlab/math/parameterizing-functions.html

[Ben Smith]

Is there a way of doing

 options = optimoptions(@fminunc,'StepTolerance',0.01); 

But for fminsearch? because i cant see anything like that in the possible fields of optimset?

[Walter Roberson]

https://www.mathworks.com/help/matlab/ref/fminsearch.html#bvadxhn-1-options

TolX would sound to be something you could use for that.