source leaprc.gaff
source leaprc.water.tip3p
loadamberparams frcmod.ionsjc_tip3p

# Load force field
loadamberparams COMPLEX_1HE.frcmod
loadamberparams COMPLEX_2HE.frcmod
loadamberparams COMPLEX_3HE.frcmod
# Load protein force field
source leaprc.protein.ff19SB
# Load library for residues and metal
loadoff COMPLEX.lib


PRO = loadpdb "easyPARM_MetalloProtein_Final.pdb"

# Define bonds for the metal coordination and Link adjacent residues
bond PRO.82.Fe1 PRO.23.NE2
bond PRO.82.Fe1 PRO.36.NE2
bond PRO.82.C18 PRO.32.SG
bond PRO.82.C25 PRO.35.SG
bond PRO.34.C PRO.35.N
bond PRO.31.C PRO.32.N
bond PRO.35.C PRO.36.N
bond PRO.23.C PRO.24.N
bond PRO.22.C PRO.23.N
bond PRO.36.C PRO.37.N
bond PRO.32.C PRO.33.N
bond PRO.83.Fe1 PRO.26.NE2
bond PRO.83.Fe1 PRO.64.NE2
bond PRO.83.C18 PRO.60.SG
bond PRO.83.C25 PRO.63.SG
bond PRO.62.C PRO.63.N
bond PRO.26.C PRO.27.N
bond PRO.63.C PRO.64.N
bond PRO.64.C PRO.65.N
bond PRO.59.C PRO.60.N
bond PRO.25.C PRO.26.N
bond PRO.60.C PRO.61.N
bond PRO.84.Fe1 PRO.51.SD
bond PRO.84.Fe1 PRO.80.NE2
bond PRO.84.C18 PRO.76.SG
bond PRO.84.C25 PRO.79.SG
bond PRO.51.C PRO.52.N
bond PRO.80.C PRO.81.N
bond PRO.50.C PRO.51.N
bond PRO.76.C PRO.77.N
bond PRO.79.C PRO.80.N
bond PRO.75.C PRO.76.N
bond PRO.78.C PRO.79.N

# Save vacuum files
savepdb PRO 1RWJ_vacuum.pdb
saveamberparm PRO 1RWJ_vacuum.prmtop 1RWJ_vacumm.inpcrd
# Solvate the system
solvateoct PRO TIP3PBOX 10.0
check PRO charge
addions PRO Cl- 0.
addions PRO Na+ 0.
# Save solvated files
saveamberparm PRO1 1RWJ_solvated.prmtop 1RWJ_solvated.inpcrd
savepdb PRO1 1RWJ_solvated.pdb
quit