#!/bin/bash
na=A_smr_A
rad=10

cat <<eof> file 
source leaprc.protein.ff14SB
source leaprc.GLYCAM_06j-1
loadAmberPrep smr.prepin
loadAmberParams frcmod.ionsjc_tip3p
loadAmberParams frcmod.smr
protein = loadpdb $na.pdb

saveamberparm protein $na.wa.top $na.wa.crd
savepdb protein $na.wa.pdb
quit
eof
tleap -f file