source leaprc.protein.ff14SB
source leaprc.gaff2
source leaprc.water.tip3p
addAtomTypes {
    { "Z1" "S" "sp3" }
    { "Z2" "N" "sp3" }
    { "Z3" "N" "sp3" }
    { "Z4" "N" "sp3" }
    { "Z5" "N" "sp3" }
    { "M1" "Fe" "sp3" }
}
CM1 = loadmol2 CM1.mol2
HM1 = loadmol2 HM1.mol2
FE1 = loadmol2 FE1.mol2
ILM = loadmol2 ILM.mol2
loadamberparams frcmod.ions234lm_126_tip3p
loadamberparams MetalAA3_metal.frcmod
loadamberparams ILM.frcmod
mol = loadpdb MetalAA3_metal_tleap.pdb
bond mol.461.NA mol.462.FE
bond mol.461.NB mol.462.FE
bond mol.461.NC mol.462.FE
bond mol.461.ND mol.462.FE
bond mol.400.SG mol.462.FE
bond mol.399.C mol.400.N
bond mol.400.C mol.401.N
bond mol.401.C mol.402.N
savepdb mol MetalAA3_metal_tleap_dry.pdb
saveamberparm mol MetalAA3_metal_tleap_dry.prmtop MetalAA3_metal_tleap_dry.inpcrd
solvatebox mol TIP3PBOX 10.0
addions mol Na+ 0
addions mol Cl- 0
savepdb mol MetalAA3_metal_tleap_solvated.pdb
saveamberparm mol MetalAA3_metal_tleap_solvated.prmtop MetalAA3_metal_tleap_solvated.inpcrd
quit