# Set up complex for explicit solvent simulation.

# Load AMBER '96 forcefield for protein.
source leaprc.ff96

# Load GAFF parameters.
source leaprc.gaff

# Load in protein.
receptor = loadPdb receptor.pdb

# Load parameters for ligand.
mods = loadAmberParams ligand.frcmod

# Load parameters for ligand.
loadAmberParams ligand.frcmod

# Load ligand.
ligand = loadMol2 ligand.mol2

# Create complex.
complex = combine { receptor ligand }


# Check complex.
check complex

# Report on net charge.
charge complex

# Add in explicit solvent.
solvatebox complex TIP3PBOX 8.0

# Add ions.
addions complex Cl- 0

# Check complex.
check complex

# Report on net charge.
charge complex 

# Write parameters.
saveAmberParm ligand ligand.prmtop ligand.crd
saveAmberParm receptor receptor.prmtop receptor.crd
saveAmberParm complex complex.prmtop complex.crd

# Exit
quit