source leaprc.ff03
source leaprc.gaff
loadoff benz.lib
loadoff phen.lib

complex = loadpdb complex.pdb
setbox complex vdw
savepdb complex t4_bnz_leap.pdb
saveamberparm complex t4_bnz.prm t4_bnz.rst

ligand = loadpdb ligand.pdb
setbox ligand vdw
savepdb ligand bnz_leap.pdb
saveamberparm ligand bnz.prm bnz.rst

complex = loadpdb t4_phn.pdb
setbox complex vdw
savepdb complex t4_phn_leap.pdb
saveamberparm complex t4_phn.prm t4_phn.rst

ligand = loadpdb phn.pdb
setbox ligand vdw
savepdb ligand phn_leap.pdb
saveamberparm ligand phn.prm phn.rst
