source leaprc.protein.ff19SB
source leaprc.gaff
source leaprc.water.opc
addAtomTypes {
        { "M1"  "La" "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" }
}
AN1 = loadmol2 AN1.mol2
AP1 = loadmol2 AP1.mol2
AP2 = loadmol2 AP2.mol2
TR1 = loadmol2 TR1.mol2
GU1 = loadmol2 GU1.mol2
GU2 = loadmol2 GU2.mol2
LA1 = loadmol2 LA1.mol2
loadamberparams frcmod.ionslm_126_opc
loadamberparams 8DQ2_mcpbpy.frcmod
mol = loadpdb 8DQ2_mcpbpy.pdb
set mol.111.LA pert true
bond mol.60.OD1 mol.111.LA
bond mol.62.OD1 mol.111.LA
bond mol.62.OD2 mol.111.LA
bond mol.64.OD1 mol.111.LA
bond mol.64.OD2 mol.111.LA
bond mol.66.O mol.111.LA
bond mol.68.OE1 mol.111.LA
bond mol.68.OE2 mol.111.LA
bond mol.71.OE1 mol.111.LA
bond mol.71.OE2 mol.111.LA
bond mol.59.C mol.60.N
bond mol.60.C mol.61.N
bond mol.61.C mol.62.N
bond mol.62.C mol.63.N
bond mol.63.C mol.64.N
bond mol.64.C mol.65.N
bond mol.65.C mol.66.N
bond mol.66.C mol.67.N
bond mol.67.C mol.68.N
bond mol.68.C mol.69.N
bond mol.70.C mol.71.N
bond mol.71.C mol.72.N
savepdb mol 8DQ2_dry.pdb
saveamberparm mol 8DQ2_dry.prmtop 8DQ2_dry.inpcrd
solvatebox mol OPCBOX 10.0
addions mol Na+ 0
addions mol Cl- 0
savepdb mol 8DQ2_solv.pdb
saveamberparm mol 8DQ2_solv.prmtop 8DQ2_solv.inpcrd
quit