Make sure that AMBERHOME points to /usr/local/amber12.

#
# cat leap.script 
source leaprc.ff12SB
loadamberparams frcmod.ionsjc_tip3p
test = loadPdb aligned.pdb
check test
solvateBox test TIP3PBOX 7.0 iso
addions test Na+ 2
saveAmberParm test test.prmtop test.crd
savepdb test test.pdb
#
#
# tleap -s -f leap.script
#
# vmd -dispdev text test.prmtop test.crd
set all [atomselect top all]
$all writepsf ionized.psf
quit
#
#