If you can't write a script, then do the minimization and equilibration with
water frozen in the z dimension (freeze_groups = water; freeze_dim = n n y) or
use constraints in the z dimension (posre.itp force constant 1000 along z and 0
along x and y). This will stop it from going into the membrane. Before you
start, sort the initial PDB according to z (you could do this in excel), remove
any waters that you don't want, resort according to original order, and run
pdb2gmx. Note that pope.pdb does have a small cluster of waters in the membrane.
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