source leaprc.protein.ff19SB
source leaprc.gaff
source leaprc.water.opc
addAtomTypes {
        { "M1"  "Fe" "sp3" }
        { "Y1"  "N" "sp3" }
        { "Y2"  "O" "sp3" }
        { "Y3"  "N" "sp3" }
        { "Y4"  "O" "sp3" }
        { "Y5"  "O" "sp3" }
}
HD1 = loadmol2 HD1.mol2
AP1 = loadmol2 AP1.mol2
HD2 = loadmol2 HD2.mol2
AG1 = loadmol2 AG1.mol2
FE1 = loadmol2 FE1.mol2
ZK = loadmol2 ZK.mol2
loadamberparams AKG.frcmod
loadamberparams frcmod.ions1lm_126_tip3p
loadamberparams 7JSD_mcpbpy.frcmod
mol = loadpdb 7JSD_mcpbpy.pdb
desc mol.269
bond mol.142.NE2 mol.263.FE
bond mol.144.OD1 mol.263.FE
bond mol.209.NE2 mol.263.FE
bond mol.262.O1 mol.263.FE
bond mol.262.O5 mol.263.FE
bond mol.141.C mol.142.N
bond mol.142.C mol.143.N
bond mol.143.C mol.144.N
bond mol.144.C mol.145.N
bond mol.208.C mol.209.N
bond mol.209.C mol.210.N
solvatebox mol OPCBOX 10.0
addions mol Na+ 0
addions mol Cl- 10
addions mol Na+ 10
savepdb mol hydrox_wt_solv.pdb
saveamberparm mol hydrox_wt_solv.prmtop hydrox_wt_solv.inpcrd
quit
 
