  In this article we study the MSSM with stops and Higgs scalars much lighter
than gluinos and squarks of the first two generations. In this setup, one
should use an effective field theory with partial supersymmetry in which the
gluino and heavy squarks are integrated out in order to connect SUSY parameters
(given at a high scale) to observables in the stop sector. In the construction
of this effective theory, valid below the gluino mass scale, we take into
account $O(\alpha_3)$ and $O(Y_{t,b}^2)$ effects and calculate the matching as
well as the renormalization group evolution. As a result, the running of the
parameters for the stop sector is modified with respect to the full MSSM and
SUSY relations between parameters are broken. We show that for some couplings
sizable numerical differences exist between the effective field theory approach
and the naive calculation based on the MSSM running.
