source leaprc.protein.ff14SB #Source leaprc file for ff14SB protein force field
source leaprc.gaff #Source leaprc file for gaff
source leaprc.water.tip3p #Source leaprc file for TIP3P water model
loadamberprep ligand.prepi #Load the prepi file for the ligand
loadamberparams ligand.frcmod #Load the additional frcmod file for ligand
mol = loadpdb complex_cleanh.pdb #Load PDB file for protein-ligand complex
solvatebox mol TIP3PBOX 8 #Solvate the complex with a cubic water box
addions mol Cl- 0 #Add Cl- ions to neutralize the system
saveamberparm mol complex.prmtop complex.inpcrd #Save AMBER topology and coordinate files
quit #Quit tleap program