Most of the script would be the same, only how the individual chain vectors are averaged changes. The loop with the label 'tlp' becomes

set k 1
label tlp
mantim z@K ratio r@K
mantim w@K ratio s@K
mantim z@K abs
mantim w@K abs
if k gt 40 goto skp1
mantim aav add z@K
mantim aav add w@K
goto skp2
label skp1
mantim bav add z@K
mantim bav add w@K
label skp2
incr k by 1
if k le 80 goto tlp

In this case, it is assumed that lipids 1 thru 40 are in one leaflet, and lipids 41 thru 80 are in the other.

Rick Venable
computational chemist