choderalab/protons

# Load constant ph parameters
source leaprc.constph
loadAmberParams frcmod.ionsff99_tip3p 

complex = loadPDB abl_ref.pdb

addIons2 complex Cl- 0
addIons2 complex Na+ 0

solvatebox complex TIP3PBOX 15

addIonsRand complex Na+ 35 Cl- 35 3

charge complex

check complex

# Write parameters.
saveAmberParm complex complex.prmtop complex.inpcrd

# Write PDB files
savepdb complex complex.pdb

# Exit
quit