#  ---------------------------------------------------------------------
#  Read in the force field
#  ---------------------------------------------------------------------

source leaprc.ff99SB

#  ---------------------------------------------------------------------
#  Read in definitions and partial charges for the modified residue.
#  ---------------------------------------------------------------------

loadoff arm.lib

#  ---------------------------------------------------------------------
#  Load the protein.
#  ---------------------------------------------------------------------

PDB = loadpdb myprotein.pdb

#  ---------------------------------------------------------------------
#  Make sure everything is in order.
#  ---------------------------------------------------------------------

check PDB

#  ---------------------------------------------------------------------
#  Save prmtop and coordinate files.
#  ---------------------------------------------------------------------

saveAmberParm PDB myprotein.prmtop myprotein.inpcrd

quit