Consider this untested. Leap script:

source leaprc.ff99SBildn
loadamberparams frcmod.tip4pew
loadamberparams frcmod.ionsjc_tip4pew
loadoff tip4pewbox.off
WAT = T4E 
set default FlexibleWater on
lyta = loadPdb aligned.pdb
check lyta
solvateBox lyta TIP4PEWBOX 7.0 iso
addions lyta Na+ 2
saveAmberParm lyta lyta.prmtop lyta.crd
savepdb lyta lyta.pdb
quit 

and in the namd script add

waterModel tip4