# Set up complex for explicit solvent simulation.

# Load AMBER ff99sb-ildn forcefield for protein.
source leaprc.ff99SBildn

# Load GAFF parameters for ligand.
source leaprc.gaff

# Load in protein (with all residues modeled in).
receptor = loadPdb ../../modeller/output.pdb

# Load crystal waters near this copy.
closewaters = loadPdb ../../modeller/closewater.pdb

# Add counterions
addions receptor Na+ 5

# Load ligand and parameters.
#loadAmberParams ../../antechamber/PRODRG/DRGFIN.gaff.frcmod
#ligand = loadMol2 ../../antechamber/PRODRG/DRGFIN.gaff.mol2

loadAmberParams ../../antechamber/oechem/bosutinib.gaff.frcmod
ligand = loadMol2 ../../antechamber/oechem/bosutinib.gaff.mol2

# Create complex.
complex = combine { receptor closewaters ligand }

# Check complex.
check complex

# Report on net charge.
charge ligand
charge receptor
charge complex

# Solvate ligand, receptor, and complex.
solvatebox ligand TIP3PBOX 12.0 iso
solvatebox receptor TIP3PBOX 12.0 iso
solvatebox complex TIP3PBOX 12.0 iso

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

# Exit
quit