import "gaff.lt" # The "gaff.lt" file is usually located in $MOLTEMPLATE_PATH (and is # distributed with moltemplate. See the "Installation" section in the manual.) # It contains definitions of the atoms "c2", "hc", as well as the bonded # and non-bonded interactions between them (and many other atoms). # # Moltemplate is only a simple text manipulation tool. It cannot # calculate atomic charge using quantom chemistry methods. # Atom charges for this example were taken from the OPLSAA force field file: # http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm # However, normally simulations in AMBER are assigned charges using the # "HF/6-31G* RESP2" or "AM1-BCC3" methods using AmberTools. NaSS inherits GAFF { write('Data Atoms') { $atom:S1 $mol @atom:s2 0.000 5.131 6.545 -15.487 $atom:Na1 $mol @atom:na 0.000 8.399 2.127 -18.450 $atom:O1 $mol @atom:o 0.000 7.659 4.922 -16.855 $atom:O2 $mol @atom:o 0.000 7.522 8.618 -14.546 $atom:O3 $mol @atom:o 0.000 7.455 8.882 -15.291 $atom:C1 $mol @atom:c3 0.000 -3.153 8.152 -13.117 $atom:C2 $mol @atom:c3 0.000 -0.102 8.851 -14.180 $atom:C3 $mol @atom:c3 0.000 1.868 6.332 -15.023 $atom:C4 $mol @atom:ca 0.000 0.491 3.369 -15.533 $atom:C5 $mol @atom:ca 0.000 -2.515 2.854 -14.261 $atom:C6 $mol @atom:ca 0.000 -4.689 5.307 -13.812 $atom:C7 $mol @atom:ca 0.000 -10.141 7.403 -14.795 $atom:C8 $mol @atom:ca 0.000 -7.912 4.986 -14.469 $atom:C9 $mol @atom:ca 0.000 -9.283 2.725 -16.450 $atom:H1 $mol @atom:hc 0.000 -3.834 9.586 -10.222 $atom:H2 $mol @atom:hc 0.000 -0.094 11.686 -15.872 $atom:H3 $mol @atom:hc 0.000 0.294 1.903 -18.484 $atom:H4 $mol @atom:hc 0.000 -2.406 0.378 -12.079 $atom:H5 $mol @atom:hc 0.000 -9.261 4.002 -11.619 $atom:H6 $mol @atom:hc 0.000 -12.800 9.287 -15.322 $atom:H7 $mol @atom:hc 0.000 -11.488 10.416 -14.768 $atom:H8 $mol @atom:hc 0.000 -10.899 10.110 -16.525 $atom:H9 $mol @atom:hc 0.000 -9.703 -0.222 -17.876 $atom:H10 $mol @atom:hc 0.000 -9.315 1.644 -19.568 $atom:H11 $mol @atom:hc 0.000 -11.366 0.623 -17.911 } write('Data Bond List') { $bond:C1H1 $atom:C1 $atom:H1 $bond:C1H2 $atom:C1 $atom:H2 $bond:C1H3 $atom:C1 $atom:H3 $bond:C2H7 $atom:C2 $atom:H7 $bond:C3H4 $atom:C3 $atom:H4 $bond:C3H5 $atom:C3 $atom:H5 $bond:C3H6 $atom:C3 $atom:H6 $bond:C4C5 $atom:C4 $atom:C5 $bond:C5C6 $atom:C5 $atom:C6 $bond:C6C7 $atom:C6 $atom:C7 $bond:C7C8 $atom:C7 $atom:C8 $bond:C8C9 $atom:C8 $atom:C9 $bond:C9C4 $atom:C9 $atom:C4 $bond:C5H8 $atom:C5 $atom:H8 $bond:C6H9 $atom:C6 $atom:H9 $bond:C8H10 $atom:C8 $atom:H10 $bond:C9H11 $atom:C9 $atom:H11 $bond:C7S1 $atom:C7 $atom:S1 $bond:S1O1 $atom:S1 $atom:O1 $bond:S1O2 $atom:S1 $atom:O2 $bond:S1O3 $atom:S1 $atom:O3 $bond:O3Na1 $atom:O3 $atom:Na1 } } # NaSS