source oldff/leaprc.ff14SB
source leaprc.gaff2
addAtomTypes {
        { "M1"  "Zr" "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" }
}
ZR1 = loadmol2 ZR1.mol2
LG1 = loadmol2 LG1.mol2
loadamberparams LIG.frcmod
loadamberparams frcmod.ions1lm_126_tip3p
loadamberparams ZRLIG_mcpbpy.frcmod
mol = loadpdb ZRLIG_mcpbpy.pdb
bond mol.1.ZR mol.2.O10
bond mol.1.ZR mol.2.O11
bond mol.1.ZR mol.2.O27
bond mol.1.ZR mol.2.O28
bond mol.1.ZR mol.2.O45
bond mol.1.ZR mol.2.O46
bond mol.1.ZR mol.2.O62
bond mol.1.ZR mol.2.O63
savepdb mol ZRLIG_dry.pdb
saveamberparm mol ZRLIG_dry.prmtop ZRLIG_dry.inpcrd
solvatebox mol TIP3PBOX 10.0
addions mol Na+ 0
addions mol Cl- 0
savepdb mol ZRLIG_solv.pdb
saveamberparm mol ZRLIG_solv.prmtop ZRLIG_solv.inpcrd
quit
 
