source leaprc.gaff
source leaprc.water.tip3p
loadamberparams frcmod.ionsjc_tip3p
# Define hybridization
addAtomTypes {
        { "Zn"  "Zn" "sp3" }
        { "s1"  "S" "sp3" }
        { "s2"  "S" "sp3" }
        { "n3"  "N" "sp3" }
        { "n4"  "N" "sp3" }
}
# Load force field for residues and metal
loadamberparams COMPLEX.frcmod
# Load protein force field
source leaprc.protein.ff19SB
# Load residues and metal
CY1 = loadmol2 "CY1.mol2"
CY2 = loadmol2 "CY2.mol2"
HI1 = loadmol2 "HI1.mol2"
HI2 = loadmol2 "HI2.mol2"
mol = loadmol2 "METAL.mol2"
PRO1 = loadpdb "easyPARM_MetalloProtein.pdb"
# Define bonds for the metal coordination
bond PRO1.32.Zn1 PRO1.5.SG
bond PRO1.32.Zn1 PRO1.10.SG
bond PRO1.32.Zn1 PRO1.23.NE2
bond PRO1.32.Zn1 PRO1.27.NE2
# Link adjacent residues
bond PRO1.5.N PRO1.4.C
bond PRO1.5.C PRO1.6.N
bond PRO1.10.N PRO1.9.C
bond PRO1.10.C PRO1.11.N
bond PRO1.23.N PRO1.22.C
bond PRO1.23.C PRO1.24.N
bond PRO1.27.N PRO1.26.C
bond PRO1.27.C PRO1.28.N
# Save vacuum files
savepdb PRO1 1SP2_vacuum.pdb
saveamberparm PRO1 1SP2_vacuum.prmtop 1SP2_vacumm.inpcrd
# Solvate the system
solvateoct PRO1 TIP3PBOX 10.0
check PRO1 charge
addions PRO1 Cl- 0.
addions PRO1 Na+ 0.
# Save solvated files
saveamberparm PRO1 1SP2_solvated.prmtop 1SP2_solvated.inpcrd
savepdb PRO1 1SP2_solvated.pdb
quit