source leaprc.ff14SB
addAtomTypes { { "ZN"  "Zn" "sp3" } { "S3"  "S" "sp3" } { "N2"  "N" "sp3" } }
loadoff atomic_ions.lib
loadamberparams frcmod.ions1lsm_hfe_tip3p
loadamberprep ZAFF.prep
loadamberparams ZAFF.frcmod
mol = loadpdb 2GIV_ZAFF.pdb
bond mol.98.ZN mol.34.SG
bond mol.98.ZN mol.37.SG
bond mol.98.ZN mol.50.NE2
bond mol.98.ZN mol.54.SG
savepdb mol 2GIV_ZAFF_dry.pdb
saveamberparm mol 2GIV_ZAFF_dry.prmtop 2GIV_ZAFF_dry.inpcrd
solvatebox mol TIP3PBOX 10.0
addions mol CL 0
savepdb mol 2GIV_ZAFF_solv.pdb
saveamberparm mol 2GIV_ZAFF_solv.prmtop 2GIV_ZAFF_solv.inpcrd
quit
