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