# Load GAFF parameters
source leaprc.gaff
# Load forcefield parameters
source leaprc.ff99SBildn
# Load additional ion parameters
loadoff additional_ions.lib
addPdbResMap { { 0 "Ca+" "Ca+" } { 1 "Ca+" "Ca+" } }
# Load protein.
protein = loadpdb 1Y57.modelled.pdb

# Specify disulfide bonds, if present.

# Check protein.
check protein

# Write protein parameters.
saveAmberParm protein 1Y57.prmtop 1Y57.crd

# Save as OFF library.
saveoff protein 1Y57.off