#   load atom type hybridizations
addAtomTypes {...}
#   Load the main parameter set.
parm10 = loadamberparams parm10.dat
frcmod14SB = loadamberparams frcmod.ff14SB
#   Load main chain and terminating amino acid libraries, nucleic acids
loadOff amino12.lib
loadOff aminoct12.lib
loadOff aminont12.lib
loadOff nucleic12.lib
#   Load water and ions
loadOff atomic_ions.lib
loadOff solvents.lib
HOH = TP3
WAT = TP3
#   Define the PDB name map for the amino acids and nucleic acids
addPdbResMap {...}
#  try to be good about reading in really old atom names as well:
addPdbAtomMap {...}
# assume that most often proteins use HIE
NHIS = NHIE
HIS = HIE
CHIS = CHIE

logFile leap.log
#
# ----- leaprc for loading the ff14SB force field
# ----- NOTE: this is designed for PDB format 3!
#    Uses frcmod.ff14SB for proteins; ff99bsc0 for DNA; ff99bsc0_chiOL3 for RNA
#
#   load atom type hybridizations
#
addAtomTypes {
    { "H"   "H" "sp3" }
    { "HO"  "H" "sp3" }
    { "HS"  "H" "sp3" }
    { "H1"  "H" "sp3" }
    { "H2"  "H" "sp3" }
    { "H3"  "H" "sp3" }
    { "H4"  "H" "sp3" }
    { "H5"  "H" "sp3" }
    { "HW"  "H" "sp3" }
    { "HC"  "H" "sp3" }
    { "HA"  "H" "sp3" }
    { "HP"  "H" "sp3" }
    { "HZ"  "H" "sp3" }
    { "OH"  "O" "sp3" }
    { "OS"  "O" "sp3" }
    { "O"   "O" "sp2" }
    { "O2"  "O" "sp2" }
    { "OP"  "O" "sp2" }
    { "OW"  "O" "sp3" }
    { "CT"  "C" "sp3" }
    { "CX"  "C" "sp3" }
    { "C8"  "C" "sp3" }
    { "2C"  "C" "sp3" }
    { "3C"  "C" "sp3" }
    { "CH"  "C" "sp3" }
    { "CS"  "C" "sp2" }
    { "C"   "C" "sp2" }
    { "CO"   "C" "sp2" }
    { "C*"  "C" "sp2" }
    { "CA"  "C" "sp2" }
    { "CB"  "C" "sp2" }
    { "CC"  "C" "sp2" }
    { "CN"  "C" "sp2" }
    { "CM"  "C" "sp2" }
    { "CK"  "C" "sp2" }
    { "CQ"  "C" "sp2" }
    { "CD"  "C" "sp2" }
    { "C5"  "C" "sp2" }
    { "C4"  "C" "sp2" }
    { "CP"  "C" "sp2" }
    { "CI"  "C" "sp3" }
    { "CJ"  "C" "sp2" }
    { "CW"  "C" "sp2" }
    { "CV"  "C" "sp2" }
    { "CR"  "C" "sp2" }
    { "CA"  "C" "sp2" }
    { "CY"  "C" "sp2" }
    { "C0"  "Ca" "sp3" }
    { "MG"  "Mg" "sp3" }
    { "N"   "N" "sp2" }
    { "NA"  "N" "sp2" }
    { "N2"  "N" "sp2" }
    { "N*"  "N" "sp2" }
    { "NP"  "N" "sp2" }
    { "NQ"  "N" "sp2" }
    { "NB"  "N" "sp2" }
    { "NC"  "N" "sp2" }
    { "NT"  "N" "sp3" }
    { "NY"  "N" "sp2" }
    { "N3"  "N" "sp3" }
    { "S"   "S" "sp3" }
    { "SH"  "S" "sp3" }
    { "P"   "P" "sp3" }
    { "LP"  ""  "sp3" }
    { "EP"  ""  "sp3" }
    { "F"   "F" "sp3" }
    { "Cl"  "Cl" "sp3" }
    { "Br"  "Br" "sp3" }
    { "I"   "I"  "sp3" }
    { "F-"   "F" "sp3" }
    { "Cl-"  "Cl" "sp3" }
    { "Br-"  "Br" "sp3" }
    { "I-"   "I"  "sp3" }
    { "Li+"  "Li"  "sp3" }
    { "Na+"  "Na"  "sp3" }
    { "K+"  "K"  "sp3" }
    { "Rb+"  "Rb"  "sp3" }
    { "Cs+"  "Cs"  "sp3" }
    { "Mg+"  "Mg"  "sp3" }
# glycam
    { "OG"  "O" "sp3" }
    { "OL"  "O" "sp3" }
    { "AC"  "C" "sp3" }
    { "EC"  "C" "sp3" }
}
#
#   Load the main parameter set.
#
parm10 = loadamberparams parm10.dat
frcmod14SB = loadamberparams frcmod.ff14SB
#
#   Load main chain and terminating amino acid libraries, nucleic acids
#
loadOff amino12.lib
loadOff aminoct12.lib
loadOff aminont12.lib
loadOff nucleic12.lib
#
#       Load water and ions
# 
loadOff atomic_ions.lib
loadOff solvents.lib
HOH = TP3
WAT = TP3
 
#
#   Define the PDB name map for the amino acids and nucleic acids
#
addPdbResMap {
  { 0 "HYP" "NHYP" } { 1 "HYP" "CHYP" }
  { 0 "ALA" "NALA" } { 1 "ALA" "CALA" }
  { 0 "ARG" "NARG" } { 1 "ARG" "CARG" }
  { 0 "ASN" "NASN" } { 1 "ASN" "CASN" }
  { 0 "ASP" "NASP" } { 1 "ASP" "CASP" }
  { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" }
  { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" }
  { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" }
  { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" }
  { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" }
  { 0 "HID" "NHID" } { 1 "HID" "CHID" }
  { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" }
  { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" }
  { 0 "ILE" "NILE" } { 1 "ILE" "CILE" }
  { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" }
  { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" }
  { 0 "MET" "NMET" } { 1 "MET" "CMET" }
  { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" }
  { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" }
  { 0 "SER" "NSER" } { 1 "SER" "CSER" }
  { 0 "THR" "NTHR" } { 1 "THR" "CTHR" }
  { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" }
  { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" }
  { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" }
  { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" }
  { 0 "G" "G5"  } { 1 "G" "G3"  }
  { 0 "A" "A5"  } { 1 "A" "A3"  }
  { 0 "C" "C5"  } { 1 "C" "C3"  }
  { 0 "U" "U5"  } { 1 "U" "U3"  }
  { 0 "DG" "DG5"  } { 1 "DG" "DG3"  }
  { 0 "DA" "DA5"  } { 1 "DA" "DA3"  }
  { 0 "DC" "DC5"  } { 1 "DC" "DC3"  }
  { 0 "DT" "DT5"  } { 1 "DT" "DT3"  }
#  some old Amber residue names for RNA:
  { 0  "RA5" "A5" } { 1 "RA3" "A3"} {"RA" "A" }
  { 0  "RC5" "C5" } { 1 "RC3" "C3"} {"RC" "C" }
  { 0  "RG5" "G5" } { 1 "RG3" "G3"} {"RG" "G" }
  { 0  "RU5" "U5" } { 1 "RU3" "U3"} {"RU" "U" }
#  some really old Amber residue names, assuming DNA:
  { 0 "GUA" "DG5"  } { 1 "GUA" "DG3"  } { "GUA" "DG" }
  { 0 "ADE" "DA5"  } { 1 "ADE" "DA3"  } { "ADE" "DA" }
  { 0 "CYT" "DC5"  } { 1 "CYT" "DC3"  } { "CYT" "DC" }
  { 0 "THY" "DT5"  } { 1 "THY" "DT3"  } { "THY" "DT" }
#  uncomment out the following if you have this old style RNA files:
# { 0 "GUA" "G5"  } { 1 "GUA" "G3"  } { "GUA" "G" }
# { 0 "ADE" "A5"  } { 1 "ADE" "A3"  } { "ADE" "A" }
# { 0 "CYT" "C5"  } { 1 "CYT" "C3"  } { "CYT" "C" }
# { 0 "URA" "R5"  } { 1 "URA" "R3"  } { "URA" "R" }
 
}
 
#  try to be good about reading in really old atom names as well:
addPdbAtomMap {
  { "O5*" "O5'" }
  { "C5*" "C5'" }
  { "C4*" "C4'" }
  { "O4*" "O4'" }
  { "C3*" "C3'" }
  { "O3*" "O3'" }
  { "C2*" "C2'" }
  { "O2*" "O2'" }
  { "C1*" "C1'" }
  { "C5M" "C7"  }
  { "H1*" "H1'" }
  { "H2*1" "H2'" }
  { "H2*2" "H2''" }
  { "H2'1" "H2'" }
  { "H2'2" "H2''" }
  { "H3*" "H3'" }
  { "H4*" "H4'" }
  { "H5*1" "H5'" }
  { "H5*2" "H5''" }
  { "H5'1" "H5'" }
  { "H5'2" "H5''" }
  { "HO'2" "HO2'" }
  { "H5T"  "HO5'" }
  { "H3T"  "HO3'" }
  { "O1'" "O4'" }
  { "OA"  "OP1" }
  { "OB"  "OP2" }
  { "O1P" "OP1" }
  { "O2P" "OP2" }
}
 
#
# assume that most often proteins use HIE
#
NHIS = NHIE
HIS = HIE
CHIS = CHIE

#   load atom type hybridizations
addAtomTypes {...}
#   Load the main parameter set.
parm99 = loadamberparams parm99.dat
frcmod99SB = loadamberparams frcmod.ff99SB
#   Load DNA/RNA libraries
loadOff all_nucleic94.lib
#   Load main chain and terminating 
#   amino acid libraries (i.e. ff94 libs)
loadOff all_amino94.lib
loadOff all_aminoct94.lib
loadOff all_aminont94.lib
#   Load water and ions
loadOff ions94.lib
loadOff solvents.lib
HOH = TP3
WAT = TP3
#   Define the PDB name map for the amino acids and nucleic acids
addPdbResMap {...}
#  try to be good about reading in really old atom names as well:
addPdbAtomMap {...}
# assume that most often proteins use HIE
NHIS = NHIE
HIS = HIE
CHIS = CHIE

logFile leap.log
#
# ----- leaprc for loading the ff99SB (Hornak & Simmerling) force field
# -----  this file is updated for PDB format 3
#
#   load atom type hybridizations
#
addAtomTypes {
    { "H"   "H" "sp3" }
    { "HO"  "H" "sp3" }
    { "HS"  "H" "sp3" }
    { "H1"  "H" "sp3" }
    { "H2"  "H" "sp3" }
    { "H3"  "H" "sp3" }
    { "H4"  "H" "sp3" }
    { "H5"  "H" "sp3" }
    { "HW"  "H" "sp3" }
    { "HC"  "H" "sp3" }
    { "HA"  "H" "sp3" }
    { "HP"  "H" "sp3" }
    { "OH"  "O" "sp3" }
    { "OS"  "O" "sp3" }
    { "O"   "O" "sp2" }
    { "O2"  "O" "sp2" }
    { "OW"  "O" "sp3" }
    { "CT"  "C" "sp3" }
    { "CH"  "C" "sp3" }
    { "C2"  "C" "sp3" }
    { "C3"  "C" "sp3" }
    { "C"   "C" "sp2" }
    { "C*"  "C" "sp2" }
    { "CA"  "C" "sp2" }
    { "CB"  "C" "sp2" }
    { "CC"  "C" "sp2" }
    { "CN"  "C" "sp2" }
    { "CM"  "C" "sp2" }
    { "CK"  "C" "sp2" }
    { "CQ"  "C" "sp2" }
    { "CD"  "C" "sp2" }
    { "CE"  "C" "sp2" }
    { "CF"  "C" "sp2" }
    { "CP"  "C" "sp2" }
    { "CI"  "C" "sp2" }
    { "CJ"  "C" "sp2" }
    { "CW"  "C" "sp2" }
    { "CV"  "C" "sp2" }
    { "CR"  "C" "sp2" }
    { "CA"  "C" "sp2" }
    { "CY"  "C" "sp2" }
    { "C0"  "Ca" "sp2" }
    { "MG"  "Mg" "sp3" }
    { "N"   "N" "sp2" }
    { "NA"  "N" "sp2" }
    { "N2"  "N" "sp2" }
    { "N*"  "N" "sp2" }
    { "NP"  "N" "sp2" }
    { "NQ"  "N" "sp2" }
    { "NB"  "N" "sp2" }
    { "NC"  "N" "sp2" }
    { "NT"  "N" "sp3" }
    { "N3"  "N" "sp3" }
    { "S"   "S" "sp3" }
    { "SH"  "S" "sp3" }
    { "P"   "P" "sp3" }
    { "LP"  ""  "sp3" }
    { "F"   "F" "sp3" }
    { "CL"  "Cl" "sp3" }
    { "BR"  "Br" "sp3" }
    { "I"   "I"  "sp3" }
    { "FE"  "Fe" "sp3" }
    { "EP"  ""  "sp3" }
# glycam
    { "OG"  "O" "sp3" }
    { "OL"  "O" "sp3" }
    { "AC"  "C" "sp3" }
    { "EC"  "C" "sp3" }
}
#
#   Load the main parameter set.
#
parm99 = loadamberparams parm99.dat
frcmod99SB = loadamberparams frcmod.ff99SB
#
#   Load DNA/RNA libraries
#
loadOff all_nucleic94.lib
#
#   Load main chain and terminating 
#   amino acid libraries (i.e. ff94 libs)
#
loadOff all_amino94.lib
loadOff all_aminoct94.lib
loadOff all_aminont94.lib
#
#       Load water and ions
# 
loadOff ions94.lib
loadOff solvents.lib
HOH = TP3
WAT = TP3
 
#
#   Define the PDB name map for the amino acids and DNA.
#
addPdbResMap {
  { 0 "ALA" "NALA" } { 1 "ALA" "CALA" }
  { 0 "ARG" "NARG" } { 1 "ARG" "CARG" }
  { 0 "ASN" "NASN" } { 1 "ASN" "CASN" }
  { 0 "ASP" "NASP" } { 1 "ASP" "CASP" }
  { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" }
  { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" }
  { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" }
  { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" }
  { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" }
  { 0 "HID" "NHID" } { 1 "HID" "CHID" }
  { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" }
  { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" }
  { 0 "ILE" "NILE" } { 1 "ILE" "CILE" }
  { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" }
  { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" }
  { 0 "MET" "NMET" } { 1 "MET" "CMET" }
  { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" }
  { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" }
  { 0 "SER" "NSER" } { 1 "SER" "CSER" }
  { 0 "THR" "NTHR" } { 1 "THR" "CTHR" }
  { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" }
  { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" }
  { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" }
  { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" }
  { 0 "GUA" "DG5"  } { 1 "GUA" "DG3"  } { "GUA" "DG" }
  { 0 "ADE" "DA5"  } { 1 "ADE" "DA3"  } { "ADE" "DA" }
  { 0 "CYT" "DC5"  } { 1 "CYT" "DC3"  } { "CYT" "DC" }
  { 0 "THY" "DT5"  } { 1 "THY" "DT3"  } { "THY" "DT" }
  { 0 "G" "RG5"  } { 1 "G" "RG3"  } { "G" "RG" } { "GN" "RGN" }
  { 0 "A" "RA5"  } { 1 "A" "RA3"  } { "A" "RA" } { "AN" "RAN" }
  { 0 "C" "RC5"  } { 1 "C" "RC3"  } { "C" "RC" } { "CN" "RCN" }
  { 0 "U" "RU5"  } { 1 "U" "RU3"  } { "U" "RU" } { "UN" "RUN" }
  { 0 "DG" "DG5"  } { 1 "DG" "DG3"  }
  { 0 "DA" "DA5"  } { 1 "DA" "DA3"  }
  { 0 "DC" "DC5"  } { 1 "DC" "DC3"  }
  { 0 "DT" "DT5"  } { 1 "DT" "DT3"  }
 
}
 
addPdbAtomMap {
  { "O5*" "O5'" }
  { "C5*" "C5'" }
  { "C4*" "C4'" }
  { "O4*" "O4'" }
  { "C3*" "C3'" }
  { "O3*" "O3'" }
  { "C2*" "C2'" }
  { "C1*" "C1'" }
  { "C5M" "C7"  }
  { "O2*" "O2'" }
  { "H1*" "H1'" }
  { "H2*1" "H2'1" }
  { "H2*2" "H2'2" }
  { "H2'"  "H2'1" }
  { "H2''" "H2'2" }
  { "H3*" "H3'" }
  { "H4*" "H4'" }
  { "H5*1" "H5'1" }
  { "H5*2" "H5'2" }
  { "H5'"  "H5'1" }
  { "H5''" "H5'2" }
  { "HO2'" "HO'2" }
  { "HO5'" "H5T" }
  { "HO3'" "H3T" }
  { "O1'" "O4'" }
  { "OA"  "O1P" }
  { "OB"  "O2P" }
  { "OP1" "O1P" }
  { "OP2" "O2P" }
}
 
 
#
# assumed that most often proteins use HIE
#
NHIS = NHIE
HIS = HIE
CHIS = CHIE

logFile leap.log
#
# ----- leaprc for loading the general Amber Force field.
#       This file is mostly for use with Antechamber
#
#   load atom type hybridizations
#
addAtomTypes {
    { "h1"  "H" "sp3" }
    { "h2"  "H" "sp3" }
    { "h3"  "H" "sp3" }
    { "h4"  "H" "sp3" }
    { "h5"  "H" "sp3" }
    { "ha"  "H" "sp3" }
    { "hc"  "H" "sp3" }
    { "hn"  "H" "sp3" }
    { "ho"  "H" "sp3" }
    { "hp"  "H" "sp3" }
    { "hs"  "H" "sp3" }
    { "hw"  "H" "sp3" }
    { "hx"  "H" "sp3" }
    { "o"  "O" "sp2" }
    { "o2"  "O" "sp2" }
    { "oh"  "O" "sp3" }
    { "os"  "O" "sp3" }
    { "ow"  "O" "sp3" }
    { "c"  "C" "sp2" }
    { "c1"  "C" "sp2" }
    { "c2"  "C" "sp2" }
    { "c3"  "C" "sp3" }
    { "ca"  "C" "sp2" }
    { "cc"  "C" "sp2" }
    { "cd"  "C" "sp2" }
    { "ce"  "C" "sp2" }
    { "cf"  "C" "sp2" }
    { "cg"  "C" "sp2" }
    { "ch"  "C" "sp2" }
    { "cp"  "C" "sp2" }
    { "cq"  "C" "sp2" }
    { "cu"  "C" "sp2" }
    { "cv"  "C" "sp2" }
    { "cx"  "C" "sp2" }
    { "cy"  "C" "sp2" }
    { "cz"  "C" "sp2" }
    { "n"   "N" "sp2" }
    { "n1"  "N" "sp2" }
    { "n2"  "N" "sp2" }
    { "n3"  "N" "sp3" }
    { "n4"  "N" "sp3" }
    { "na"  "N" "sp2" }
    { "nb"  "N" "sp2" }
    { "nc"  "N" "sp2" }
    { "nd"  "N" "sp2" }
    { "ne"  "N" "sp2" }
    { "nf"  "N" "sp2" }
    { "nh"  "N" "sp2" }
    { "no"  "N" "sp2" }
    { "s"   "S" "sp2" }
    { "s2"   "S" "sp2" }
    { "s3"   "S" "sp3" }
    { "s4"   "S" "sp3" }
    { "s6"   "S" "sp3" }
    { "sh"   "S" "sp3" }
    { "ss"   "S" "sp3" }
    { "sx"   "S" "sp3" }
    { "sy"   "S" "sp3" }
    { "p2"   "P" "sp2" }
    { "p3"   "P" "sp3" }
    { "p4"   "P" "sp3" }
    { "p5"   "P" "sp3" }
    { "pb"   "P" "sp3" }
    { "pc"   "P" "sp3" }
    { "pd"   "P" "sp3" }
    { "pe"   "P" "sp3" }
    { "pf"   "P" "sp3" }
    { "px"   "P" "sp3" }
    { "py"   "P" "sp3" }
    { "f"   "F" "sp3" }
    { "cl"  "Cl" "sp3" }
    { "br"  "Br" "sp3" }
    { "i"   "I"  "sp3" }
}
#
#   Load the general force field parameter set.
#
gaff = loadamberparams gaff.dat