source oldff/leaprc.ff14SB
source leaprc.gaff
source leaprc.water.tip3p
addAtomTypes {
        { "M1"  "Mg" "sp3" }
        { "M2"  "Mg" "sp3" }
        { "M3"  "Mg" "sp3" }
        { "Y1"  "O" "sp3" }
        { "Y2"  "O" "sp3" }
        { "Y3"  "O" "sp3" }
        { "Y4"  "O" "sp3" }
        { "Y5"  "O" "sp3" }
        { "Y6"  "O" "sp3" }
        { "Y7"  "O" "sp3" }
        { "Y8"  "O" "sp3" }
        { "Y9"  "O" "sp3" }
        { "Z1"  "O" "sp3" }
        { "Z2"  "O" "sp3" }
        { "Z3"  "O" "sp3" }
        { "Z4"  "O" "sp3" }
        { "Z5"  "O" "sp3" }
        { "Z6"  "O" "sp3" }
        { "Z7"  "O" "sp3" }
}
AP1 = loadmol2 AP1.mol2
AN1 = loadmol2 AN1.mol2
SR1 = loadmol2 SR1.mol2
GU1 = loadmol2 GU1.mol2
MG1 = loadmol2 MG1.mol2
MG2 = loadmol2 MG2.mol2
MG3 = loadmol2 MG3.mol2
PP1 = loadmol2 PP1.mol2
WT1 = loadmol2 WT1.mol2
WT2 = loadmol2 WT2.mol2
WT3 = loadmol2 WT3.mol2
WT4 = loadmol2 WT4.mol2
WT5 = loadmol2 WT5.mol2
WT6 = loadmol2 WT6.mol2
WT7 = loadmol2 WT7.mol2
loadamberparams POP.frcmod
loadamberparams frcmod.ions1lm_126_tip3p
loadamberparams 6OFV_mcpbpy.frcmod
mol = loadpdb 6OFV_mcpbpy.pdb
bond mol.84.OD1 mol.341.MG
bond mol.84.OD2 mol.342.MG
bond mol.225.OD1 mol.343.MG
bond mol.229.OG mol.343.MG
bond mol.233.OE2 mol.343.MG
bond mol.341.MG mol.344.O2
bond mol.341.MG mol.345.O
bond mol.341.MG mol.347.O
bond mol.341.MG mol.349.O
bond mol.341.MG mol.350.O
bond mol.342.MG mol.344.O2
bond mol.342.MG mol.344.O6
bond mol.342.MG mol.346.O
bond mol.342.MG mol.349.O
bond mol.342.MG mol.351.O
bond mol.343.MG mol.344.O1
bond mol.343.MG mol.344.O4
bond mol.343.MG mol.348.O
bond mol.83.C mol.84.N
bond mol.84.C mol.85.N
bond mol.224.C mol.225.N
bond mol.225.C mol.226.N
bond mol.228.C mol.229.N
bond mol.229.C mol.230.N
bond mol.232.C mol.233.N
bond mol.233.C mol.234.N
savepdb mol 6OFV_dry.pdb
saveamberparm mol 6OFV_dry.prmtop 6OFV_dry.inpcrd
solvatebox mol TIP3PBOX 10.0
addions mol Na+ 0
addions mol Cl- 0
savepdb mol 6OFV_solv.pdb
saveamberparm mol 6OFV_solv.prmtop 6OFV_solv.inpcrd
quit
 
