# Load force field parameters

source leaprc.gaff

source leaprc.ff99SB

# Load Antechamber files - from 3.8

loadAmberPrep pope.prepin

loadAmberParams pope.frcmod

# Load positioned binding pocket ions - from 3.5

bpions = loadpdb “bp_ions_positioned.pdb”

# Load positioned LeuT with missing residues - from 3.6

leut = loadpdb “leut_positioned_allres.pdb”

# Load lipids and lipid solvation - from 3.7

pope = loadpdb “pope.pdb”

popewater = loadpdb “pope_water.pdb”

# Combine into one unit

system = combine {bpions leut pope popewater}

# Set periodic box

setBox system vdw

# Solvate the system along the z axis; maintain a distance of 1.5 A from solute

solvateBox system TIP3PBOX {0 0 12} 1.5

# Add ions to produce a neutral system

addIons system Na+ 56 Cl- 60

# Examine the final unit

check system

charge system

desc system

# Output files

savePdb system leut_system.pdb

saveamberparm system leut_system.prmtop leut_system.inpcrd

quit