logFile leap.log
#
# -- leaprc file of the INTERFACE force field (v1.5) for AMBER
#
# Referred from the INTERFACE force field (v1.5) files downloaded from:
#    https://bionanostructures.com/interface-md/
#
# References:
#   Neutral Face Centered Cubic (FCC) Metals
#     J. Phys. Chem. C 2008, 112, 17281-17290
#   Silica (Bulk and Surfaces of Q2, Q3, and Q4 Chemistry with Different Ionization)
#     Chem. Mater., 2014, 26, 2647-2658
#   Clay Minerals (Kaolinite, Mica, Montmorillonites, Pyrophyllite)
#     Chem. Mater., 2005, 17, 5658-5669 & Extension to Kaolinite
#   Cement Minerals (Tricalcium Silicate, Tricalcium Aluminate)
#     J. Phys. Chem. C 2013, 117, 10417-10432
#     Dalton Trans. 2014, 43, 10602-10616
#   Apatite (Bulk and Surfaces of Hydroxyapatite for Different Protonation/PH)
#     Langmuir 2013, 29, 1754-1765
#     Tzu-Jen Lin PhD Thesis, U of Akron 2013
#     J. Phys. Cond. Mat. 2014, 26, 244105
#
# ------------------  Atom Type Table  ------------------
# Original Atom Type| New Atom Type in| 
# in the INTERFACE  | the AMBER Force |  Material Types
# Force Field       | Field           |
#      HOC          |       01        |  Cement Minerals
#      HOK          |       02        |  Clay Minerals
#      HOP          |       03        |  Apatite
#      HOY          |       04        |  Silica, Clay Minerals
#     OAP1          |       11        |  Apatite
#     OAP2          |       12        |  Apatite
#      OC1          |       13        |  Cement Minerals
#      OC2          |       14        |  Cement Minerals
#      OC3          |       15        |  Cement Minerals
#      OC4          |       16        |  Cement Minerals
#      OC5          |       17        |  Cement Minerals
#     OC23          |       18        |  Silica
#     OC24          |       19        |  Silica
#      OY1          |       20        |  Clay Minerals
#      OY2          |       21        |  Clay Minerals
#      OY3          |       22        |  Clay Minerals
#      OY4          |       23        |  Clay Minerals
#      OY5          |       24        |  Clay Minerals
#      OY6          |       25        |  Clay Minerals
#      OY7          |       26        |  Clay Minerals
#      OY8          |       27        |  Clay Minerals
#      OY9          |       28        |  Clay Minerals
#      AC1          |       41        |  Cement Minerals
#      AY1          |       42        |  Clay Minerals
#      AY2          |       43        |  Clay Minerals
#     AYT1          |       44        |  Clay Minerals
#     AYT2          |       45        |  Clay Minerals
#      SC1          |       51        |  Cement Minerals
#      SC4          |       52        |  Silica
#      SY1          |       53        |  Clay Minerals
#      SY2          |       54        |  Clay Minerals
#      PAP          |       61        |  Apatite
#      NA+          |       NAp       |  Silica, Clay Minerals
#       K+          |       Kp        |  Clay Minerals
#     CA++          |       CApp      |  Cement Minerals
#     CA+A          |       CApA      |  Cement Minerals
#     CA+H          |       CApH      |  Apatite
#       AL          |       Al0       |  FCC Metals
#       NI          |       Ni0       |  FCC Metals
#       CU          |       Cu0       |  FCC Metals
#       PD          |       Pd0       |  FCC Metals
#       AG          |       Ag0       |  FCC Metals
#       PT          |       Pt0       |  FCC Metals
#       AU          |       Au0       |  FCC Metals
#       PB          |       Pb0       |  FCC Metals
# -----------------  -----------------  -----------------
# load atom type hybridization
#
addAtomTypes {
    { "01" "H"  "sp3"}
    { "02" "H"  "sp3"}
    { "03" "H"  "sp3"}
    { "04" "H"  "sp3"}
    { "11" "O"  "sp3"}
    { "12" "O"  "sp3"}
    { "13" "O"  "sp3"}
    { "14" "O"  "sp3"}
    { "15" "O"  "sp3"}
    { "16" "O"  "sp3"}
    { "17" "O"  "sp3"}
    { "18" "O"  "sp3"}
    { "19" "O"  "sp3"}
    { "20" "O"  "sp3"}
    { "21" "O"  "sp3"}
    { "22" "O"  "sp3"}
    { "23" "O"  "sp3"}
    { "24" "O"  "sp3"}
    { "25" "O"  "sp3"}
    { "26" "O"  "sp3"}
    { "27" "O"  "sp3"}
    { "28" "O"  "sp3"}
    { "41" "Al"  "sp3"}
    { "42" "Al"  "sp3"}
    { "43" "Al"  "sp3"}
    { "44" "Al"  "sp3"}
    { "45" "Al"  "sp3"}
    { "51" "Si"  "sp3"}
    { "52" "Si"  "sp3"}
    { "53" "Si"  "sp3"}
    { "54" "Si"  "sp3"}
    { "61" "P"  "sp3"}
    { "NAp" "Na"  "sp3"}
    { "Kp" "K"  "sp3"}
    { "CApp" "Ca"  "sp3"}
    { "CApA" "Ca"  "sp3"}
    { "CApH" "Ca"  "sp3"}
    { "Al0" "Al"  "sp3"}
    { "Ni0" "Ni"  "sp3"}
    { "Cu0" "Cu"  "sp3"}
    { "Pd0" "Pd"  "sp3"}
    { "Ag0" "Ag"  "sp3"}
    { "Pt0" "Pt"  "sp3"}
    { "Au0" "Au"  "sp3"}
    { "Pb0" "Pb"  "sp3"}
    { "HW" "H"  "sp3"}
    { "OW" "O"  "sp3"}
}
#
#   Load the INTERFACE force field parameter
#
interface = loadamberparams interface_v1_5.dat

#   Load the FCC metals library
LoadOff fcc_metals.lib