remarks file toppar/ion.top
remarks topology and masses for common ions
remarks Dingle atom ion residues are given the name of the element.
remarks By default the atom will be uncharged (eg. the residue MG will
remarks contain the atom called MG with zero charge).
remarks To use the charged species the charge state is appended to
remarks the atom name (eg to use MG2+ the residue name is MG2, and the
remarks atom name is MG+2 and has charge +2.0).
remarks NOTE: not all ionic species are represented
remarks PDA 02/09/99

set echo=false end

checkversion 1.2

autogenerate  angles=true  end

MASS  LI      6.9410   ! lithium
MASS   F     18.9984   ! fluorine
MASS  NA     22.9898   ! sodium   
MASS  MG     24.3050   ! magnesium
MASS  AL     26.9815   ! aluminum
MASS  CL     35.4530   ! chlorine 
MASS   K     39.0980   ! potassium
MASS  AR     39.9480   ! argon
MASS  CA     40.0800   ! calcium  
MASS   V     50.9415   ! vanadium
MASS  CR     51.9960   ! chromium
MASS  MN     54.9380   ! manganese
MASS  FE     55.8470   ! iron     
MASS  NI     58.6900   ! nickel
MASS  CO     58.9332   ! cobalt
MASS  CU     63.5460   ! copper   
MASS  ZN     65.3700   ! zinc     
MASS  AS     74.9216   ! arsenic
MASS  BR     79.9040   ! bromine
MASS  KR     83.8000   ! krypton
MASS  SR     87.6200   ! strontium
MASS  MO     95.9400   ! molybdenum
MASS  AG    107.8680   ! silver
MASS  CD    112.4100   ! cadmium
MASS   I    126.9045   ! iodine
MASS  XE    131.2900   ! xenon
MASS  CS    132.9054   ! cesium
MASS  HO    164.9304   ! holmium
MASS  YB    173.0400   ! ytterbium
MASS  OS    190.2000   ! osmium
MASS  IR    192.2200   ! iridium
MASS  PT    195.0800   ! platinum 
MASS  AU    196.9665   ! gold     
MASS  HG    200.5900   ! mercury
MASS  PB    207.2000   ! lead
MASS   U    238.0289   ! uranium

MASS  LI+1    6.9410   ! lithium 1+
MASS   F-1   18.9984   ! fluorine 1-
MASS  NA+1   22.9898   ! sodium 1+
MASS  MG+2   24.3050   ! magnesium 2+
MASS  AL+3   26.9815   ! aluminum 3+
MASS  CL-1   35.4530   ! chloride 1-
MASS   K+1   39.0980   ! potassium 1+
MASS  CA+2   40.0800   ! calcium 2+
MASS   V+2   50.9415   ! vanadium 2+
MASS   V+3   50.9415   ! vanadium 3+
MASS  CR+2   51.9960   ! chromium 2+
MASS  CR+3   51.9960   ! chromium 3+
MASS  MN+2   54.9380   ! manganese 2+
MASS  MN+3   54.9380   ! manganese 3+
MASS  FE+2   55.8470   ! iron 2+
MASS  FE+3   55.8470   ! iron 3+  
MASS  NI+2   58.6900   ! nickel 2+
MASS  CO+2   58.9332   ! cobalt 2+
MASS  CO+3   58.9332   ! cobalt 3+
MASS  CU+1   63.5460   ! copper 1+
MASS  CU+2   63.5460   ! copper 2+
MASS  ZN+2   65.3700   ! zinc 2+
MASS  BR-1   79.9040   ! bromine 1-
MASS  SR+2   87.6200   ! strontium 2+
MASS  MO+3   95.9400   ! molybdenum 3+
MASS  AG+1  107.8680   ! silver 1+
MASS  CD+2  112.4100   ! cadmium 2+
MASS   I-1  126.9045   ! iodine 1-
MASS  CS+1  132.9054   ! cesium 1+
MASS  HO+3  164.9304   ! holmium 3+
MASS  YB+2  173.0400   ! ytterbium 2+
MASS  YB+3  173.0400   ! ytterbium 3+
MASS  OS+4  190.2000   ! osmium 4+
MASS  IR+3  192.2200   ! iridium 3+
MASS  PT+2  195.0800   ! platinum 2+
MASS  AU+1  196.9665   ! gold 1+    
MASS  AU+3  196.9665   ! gold 3+    
MASS  HG+1  200.5900   ! mercury 1+
MASS  HG+2  200.5900   ! mercury 2+
MASS  PB+2  207.2000   ! lead 2+
MASS   U+3  238.0289   ! uranium 3+
MASS   U+4  238.0289   ! uranium 4+

MASS  SUF    32.0600   ! sulphate anion sulphur 
MASS  OUF    15.9994   ! sulphate anion oxygen
MASS  PHF    30.9740   ! phosphate anion phosphorus
MASS  OHF    15.9994   ! phosphate anion oxygen
MASS  W     184.0000   ! tungstate anion tungsten
MASS  OWF    15.9994   ! tungstate anion oxygen

{- ========================== uncharged states ============================ -}

RESIdue F {fluorine}
  GROUp
    ATOM F TYPE=F CHARge=0.0 END
END {F}

RESIdue NA {sodium}
  GROUp
    ATOM NA TYPE=NA CHARge=0.0 END
END {NA}

RESIdue MG {magnesium}
  GROUp
    ATOM MG TYPE=MG CHARge=0.0 END
END {MG}

RESIdue AL {aluminum}
  GROUp
    ATOM AL TYPE=AL CHARge=0.0 END
END {AL}

RESIdue CL {chlorine}
  GROUp
    ATOM CL TYPE=CL CHARge=0.0 END
END {CL}

RESIdue K {potassium}
  GROUp
    ATOM K TYPE=K CHARge=0.0 END
END {K}

RESIdue AR {argon}
  GROUp
    ATOM AR TYPE=AR CHARge=0.0 END
END {AR}

RESIdue CA {calcium}
  GROUp
    ATOM CA TYPE=CA CHARge=0.0 END
END {CA}

RESIdue V {vanadium}
  GROUp
    ATOM V TYPE=V CHARge=0.0 END
END {V}

RESIdue CR {chromium}
  GROUp
    ATOM CR TYPE=CR CHARge=0.0 END
END {CR}

RESIdue MN {manganese}
  GROUp
    ATOM MN TYPE=MN CHARge=0.0 END
END {MN}

RESIdue FE {iron}
  GROUp
    ATOM FE TYPE=FE CHARge=0.0 END
END {FE}

RESIdue NI {nickel}
  GROUp
    ATOM NI TYPE=NI CHARge=0.0 END
END {NI}

RESIdue CO {cobalt}
  GROUp
    ATOM CO TYPE=CO CHARge=0.0 END
END {CO}

RESIdue CU {copper}
  GROUp
    ATOM CU TYPE=CU CHARge=0.0 END
END {CU}

RESIdue ZN {zinc}
  GROUp
    ATOM ZN TYPE=ZN CHARge=0.0 END
END {ZN}

RESIdue AS {arsenic}
  GROUp
    ATOM AS TYPE=AS CHARge=0.0 END
END {AS}

RESIdue BR {bromine}
  GROUp
    ATOM BR TYPE=BR CHARge=0.0 END
END {BR}

RESIdue KR {krypton}
  GROUp
    ATOM KR TYPE=KR CHARge=0.0 END
END {KR}

RESIdue SR {strontium}
  GROUp
    ATOM SR TYPE=SR CHARge=0.0 END
END {SR}

RESIdue MO {molybdenum}
  GROUp
    ATOM MO TYPE=MO CHARge=0.0 END
END {MO}

RESIdue AG {silver}
  GROUp
    ATOM AG TYPE=AG CHARge=0.0 END
END {AG}

RESIdue CD {cadmium}
  GROUp
    ATOM CD TYPE=CD CHARge=0.0 END
END {CD}

RESIdue I {iodine}
  GROUp
    ATOM I TYPE=I CHARge=0.0 END
END {I}

RESIdue XE {xenon}
  GROUp
    ATOM XE TYPE=XE CHARge=0.0 END
END {XE}

RESIdue CS {cesium}
  GROUp
    ATOM CS TYPE=CS CHARge=0.0 END
END {CS}

RESIdue HO {holmium}
  GROUp
    ATOM HO TYPE=HO CHARge=0.0 END
END {HO}

RESIdue YB {ytterbium}
  GROUp
    ATOM YB TYPE=YB CHARge=0.0 END
END {YB}

RESIdue OS {osmium}
  GROUp
    ATOM OS TYPE=OS CHARge=0.0 END
END {OS}

RESIdue IR {iridium}
  GROUp
    ATOM IR TYPE=IR CHARge=0.0 END
END {IR}

RESIdue PT {platinum}
  GROUp
    ATOM PT TYPE=PT CHARge=0.0 END
END {PT}

RESIdue AU {gold}
  GROUp
    ATOM AU TYPE=AU CHARge=0.0 END
END {AU}

RESIdue HG {mercury}
  GROUp
    ATOM HG TYPE=HG CHARge=0.0 END
END {HG}

RESIdue PB {lead}
  GROUp
    ATOM PB TYPE=PB CHARge=0.0 END
END {PB}

RESIdue U {uranium}
  GROUp
    ATOM U TYPE=U CHARge=0.0 END
END {U}

{- ============================ ionic states ============================== -}

RESIdue LI1 {lithium 1+}
  GROUp
    ATOM LI+1 TYPE=LI+1 CHARge=+1.0 END
END {LI1}

RESIdue F1 {fluorine 1-}
  GROUp
    ATOM F-1 TYPE=F-1 CHARge=-1.0 END
END {F1}

RESIdue NA1 {sodium 1+}
  GROUp
    ATOM NA+1 TYPE=NA+1 CHARge=+1.0 END
END {NA1}

RESIdue MG2 {magnesium 2+}
  GROUp
    ATOM MG+2 TYPE=MG+2 CHARge=+2.0 END
END {MG2}

RESIdue AL3 {aluminum 3+}
  GROUp
    ATOM AL+3 TYPE=AL+3 CHARge=+3.0 END
END {AL3}

RESIdue CL1 {chloride 1-}
  GROUp
    ATOM CL-1 TYPE=CL-1 CHARge=-1.0 END
END {CL1}

RESIdue K1 {potassium 1+}
  GROUp
    ATOM K+1 TYPE=K+1 CHARge=+1.0 END
END {K1}

RESIdue CA2 {calcium 2+}
  GROUp
    ATOM CA+2 TYPE=CA+2 CHARge=+2.0 END
END {CA2}

RESIdue V2 {vanadium 2+}
  GROUp
    ATOM V+2 TYPE=V+2 CHARge=+2.0 END
END {V2}

RESIdue V3 {vanadium 3+}
  GROUp
    ATOM V+3 TYPE=V+3 CHARge=+3.0 END
END {V3}

RESIdue CR2 {chromium 2+}
  GROUp
    ATOM CR+2 TYPE=CR+2 CHARge=+2.0 END
END {CR2}

RESIdue CR3 {chromium 3+}
  GROUp
    ATOM CR+3 TYPE=CR+3 CHARge=+3.0 END
END {CR3}

RESIdue MN2 {manganese 2+}
  GROUp
    ATOM MN+2 TYPE=MN+2 CHARge=+2.0 END
END {MN2}

RESIdue MN3 {manganese 3+}
  GROUp
    ATOM MN+3 TYPE=MN+3 CHARge=+3.0 END
END {MN3}

RESIdue FE2 {iron 2+}
  GROUp
    ATOM FE+2 TYPE=FE+2 CHARge=+2.0 END
END {FE2}

RESIdue FE3 {iron 3+}
  GROUp
    ATOM FE+3 TYPE=FE+3 CHARge=+3.0 END
END {FE3}

RESIdue NI2 {nickel 2+}
  GROUp
    ATOM NI+2 TYPE=NI+2 CHARge=+2.0 END
END {NI2}

RESIdue CO2 {cobalt 2+}
  GROUp
    ATOM CO+2 TYPE=CO+2 CHARge=+2.0 END
END {CO2}

RESIdue CO3 {cobalt 3+}
  GROUp
    ATOM CO+3 TYPE=CO+3 CHARge=+3.0 END
END {CO3}

RESIdue CU1 {copper 1+}
  GROUp
    ATOM CU+1 TYPE=CU+1 CHARge=+1.0 END
END {CU1}

RESIdue CU2 {copper 2+}
  GROUp
    ATOM CU+2 TYPE=CU+2 CHARge=+2.0 END
END {CU2}

RESIdue ZN2 {zinc 2+}
  GROUp
    ATOM ZN+2 TYPE=ZN+2 CHARge=+2.0 END
END {ZN2}

RESIdue BR1 {bromine 1-}
  GROUp
    ATOM BR-1 TYPE=BR-1 CHARge=-1.0 END
END {BR1}

RESIdue SR2 {strontium 2+}
  GROUp
    ATOM SR+2 TYPE=SR+2 CHARge=+2.0 END
END {SR2}

RESIdue MO3 {molybdenum 3+}
  GROUp
    ATOM MO+3 TYPE=MO+3 CHARge=+3.0 END
END {MO3}

RESIdue AG1 {silver 1+}
  GROUp
    ATOM AG+1 TYPE=AG+1 CHARge=+1.0 END
END {AG1}

RESIdue CD2 {cadmium 2+}
  GROUp
    ATOM CD+2 TYPE=CD+2 CHARge=+2.0 END
END {CD2}

RESIdue I1 {iodine 1-}
  GROUp
    ATOM I-1 TYPE=I-1 CHARge=-1.0 END
END {I1}

RESIdue CS1 {cesium 1+}
  GROUp
    ATOM CS+1 TYPE=CS+1 CHARge=+1.0 END
END {CS1}

RESIdue HO3 {holmium 3+}
  GROUp
    ATOM HO+3 TYPE=HO+3 CHARge=+3.0 END
END {HO3}

RESIdue YB2 {ytterbium 2+}
  GROUp
    ATOM YB+2 TYPE=YB+2 CHARge=+2.0 END
END {YB2}

RESIdue YB3 {ytterbium 3+}
  GROUp
    ATOM YB+3 TYPE=YB+3 CHARge=+3.0 END
END {YB3}

RESIdue OS4 {osmium 4+}
  GROUp
    ATOM OS+4 TYPE=OS+4 CHARge=+4.0 END
END {OS4}

RESIdue IR3 {iridium 3+}
  GROUp
    ATOM IR+3 TYPE=IR+3 CHARge=+3.0 END
END {IR3}

RESIdue PT2 {platinum 2+}
  GROUp
    ATOM PT+2 TYPE=PT+2 CHARge=+2.0 END
END {PT2}

RESIdue AU1 {gold 1+}
  GROUp
    ATOM AU+1 TYPE=AU+1 CHARge=+1.0 END
END {AU1}

RESIdue AU3 {gold 3+}
  GROUp
    ATOM AU+3 TYPE=AU+3 CHARge=+3.0 END
END {AU3}

RESIdue HG1 {mercury 1+}
  GROUp
    ATOM HG+1 TYPE=HG+1 CHARge=+1.0 END
END {HG1}

RESIdue HG2 {mercury 2+}
  GROUp
    ATOM HG+2 TYPE=HG+2 CHARge=+2.0 END
END {HG2}

RESIdue PB2 {lead 2+}
  GROUp
    ATOM PB+2 TYPE=PB+2 CHARge=+2.0 END
END {PB2}

RESIdue U3 {uranium 3+}
  GROUp
    ATOM U+3 TYPE=U+3 CHARge=+3.0 END
END {U3}

RESIdue U4 {uranium 4+}
  GROUp
    ATOM U+4 TYPE=U+4 CHARge=+4.0 END
END {U4}

{- ========================= multi-atom species =========================== -}

RESIdue SO4 {Sulphate}
  GROUP
    ATOM S  TYPE=SUF CHARGE=+2.0 END
    ATOM O1 TYPE=OUF CHARGE=-1.0 END
    ATOM O2 TYPE=OUF CHARGE=-1.0 END
    ATOM O3 TYPE=OUF CHARGE=-1.0 END
    ATOM O4 TYPE=OUF CHARGE=-1.0 END

  BOND S  O1
  BOND S  O2
  BOND S  O3
  BOND S  O4

END {SO4}

RESIdue PO4 {Phosphate}
  GROUP
    ATOM P  TYPE=PHF CHARGE=+2.0 END
    ATOM O1 TYPE=OHF CHARGE=-1.0 END
    ATOM O2 TYPE=OHF CHARGE=-1.0 END
    ATOM O3 TYPE=OHF CHARGE=-1.0 END
    ATOM O4 TYPE=OHF CHARGE=-1.0 END

  BOND P  O1
  BOND P  O2
  BOND P  O3
  BOND P  O4

END {PO4}

RESIdue WO4 {Tungstate}
  GROUP
    ATOM W  TYPE=W   CHARGE=+2.0 END
    ATOM O1 TYPE=OWF CHARGE=-1.0 END
    ATOM O2 TYPE=OWF CHARGE=-1.0 END
    ATOM O3 TYPE=OWF CHARGE=-1.0 END
    ATOM O4 TYPE=OWF CHARGE=-1.0 END

  BOND W  O1
  BOND W  O2
  BOND W  O3
  BOND W  O4

END {WO4}

set echo=true end