# 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

logfile leapante.log
addAtomTypes {
       { "nh"    "N"     "sp3" }
       { "c"     "C"     "sp2" }
       { "n3"    "N"     "sp3" }
       { "hn"    "H"     "sp3" }
       { "oh"    "O"     "sp3" }
       { "cc"    "C"     "sp2" }
       { "na"    "N"     "sp2" }
       { "ca"    "C"     "sp2" }
       { "nc"    "N"     "sp2" }
       { "o"     "O"     "sp2" }
       { "n"     "N"     "sp2" }
       { "cl"    "Cl"    "sp3" }
       { "ss"    "S"     "sp2" }
       { "ha"    "H"     "sp3" }
       { "h4"    "H"     "sp3" }
       { "c3"    "C"     "sp3" }
       { "hc"    "H"     "sp3" }
       { "cd"    "C"     "sp2" }
       { "nb"    "N"     "sp2" }
       { "h1"    "H"     "sp3" }
       { "ho"    "H"     "sp3" }
}
ligfrc = loadAmberParams ante_dasatinib.gaff.frcmod
lig = loadMol2 dasatinib.gaff_pchk.mol2

complex = combine { protein lig }

# Add ions.


# Add solvent.

# Specify disulfide bonds, if present.

# Check protein.
check complex

# Write protein parameters.
saveAmberParm complex complex.prmtop complex.crd