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

complex = loadpdb "1icm_ForSim.pdb"
solvatebox complex TIP3PBOX 12.0
addions complex Na+ 0
check complex
savepdb complex plm_prot.pdb

ligand = copy PLM
solvatebox ligand TIP3PBOX 12.0
addions ligand Na+ 0
check ligand
savepdb ligand plm.pdb