# Create a benzene-toluene system.

# Load parameters and ions.
parm99 = loadamberparams parm99.dat
loadOff ions94.lib
gaff = loadamberparams gaff.dat

# Create receptor.
receptor = loadmol2 benzene.gaff.mol2
receptor_params = loadamberparams benzene.frcmod
saveamberparm receptor receptor.prmtop receptor.crd

# Create ligand.
ligand = loadmol2 toluene.gaff.mol2
#translate ligand { 1.5 1.5 0 }
translate ligand { 0.01 0.01 0 }
ligand_params = loadamberparams toluene.gaff.mol2
saveamberparm ligand ligand.prmtop ligand.crd

# Create complex.
complex = combine { receptor ligand }
saveamberparm complex complex.prmtop complex.crd

quit