# Create NaCl system in explicit solvent for YANK.
source leaprc.ff99SB

# Create receptor.
receptor = loadpdb solvent.pdb

# Create ligand.
ligand = loadpdb nacl.pdb

# Create complex.
complex = combine { receptor ligand }

check complex

saveamberparm receptor receptor.prmtop receptor.crd
savepdb receptor receptor.pdb

saveamberparm ligand ligand.prmtop ligand.crd
savepdb ligand ligand.pdb

saveamberparm complex complex.prmtop complex.crd
savepdb complex complex.pdb

quit