source leaprc.ff99SB
source leaprc.gaff
loadAmberPrep "tony_myr.prep"
loadAmberPrep "tony_plm.prep"

complex = loadpdb myr_prot.pdb
setbox complex vdw
check complex
savepdb complex myr_prot_check.pdb
saveamberparm complex myr_prot.prm myr_prot.rst

ligand = loadpdb myr.pdb
setbox ligand vdw
check ligand
savepdb ligand myr_check.pdb
saveamberparm ligand myr.prm myr.rst

complex = loadpdb plm_prot.pdb
setbox complex vdw
check complex
savepdb complex plm_prot_check.pdb
saveamberparm complex plm_prot.prm plm_prot.rst

ligand = loadpdb plm.pdb
setbox ligand vdw
check ligand
savepdb ligand plm_check.pdb
saveamberparm ligand plm.prm plm.rst