# Create a benzene-toluene system in explicit TIP3P solvent.

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

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

check receptor

# 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.frcmod

check ligand

# Create complex.
complex = combine { receptor ligand }

check complex

# Solvate receptor.
solvatebox receptor TIP3PBOX 9.0
saveamberparm receptor receptor.prmtop receptor.crd

# Solvate ligand.
solvatebox ligand TIP3PBOX 9.0
saveamberparm ligand ligand.prmtop ligand.crd

# Solvate complex.
solvatebox complex TIP3PBOX 9.0
saveamberparm complex complex.prmtop complex.crd

#quit