loadAmberPrep ../my_amino94.in
source leaprc.ff96

sodiumChloride = loadPdb ../sodiumChlorideIn.pdb 

savePdb sodiumChloride sodiumChlorideOut.pdb

sodiumChloride = loadPdb sodiumChlorideOut.pdb

saveAmberParm sodiumChloride sodiumChloride.top sodiumChloride.crd

quit