source oldff/leaprc.ff14SB
loadAmberParams frcmod.ff14SB
loadAmberParams frcmod.ionsjc_tip4pew
loadAmberPrep sample.dat 
loadAmberParams sample.dat
mol = loadPdb sample.dat
bond mol.114.ZN mol.5.SG 
set mol box 12
addIons mol Cl- 0
addIons mol Na+ 0
saveAmberParm mol out/saveAmberParm_topologyfilename_9_1.prmtop out/saveAmberParm_coordinatefilename_9_2.inpcrd
savePdb mol out/savePdb_filename_10_1.pdb
quit
          