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glu.lt
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glu.lt
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import "glu_ff.lt"
glu inherits glu_ff {
# atomId molId atomType charge X Y Z
write("Data Atoms"){
$atom:O $mol:m @atom:oh -0.6161 -5.285 0.501 -1.017
$atom:C $mol:m @atom:c 0.6431 -4.861 0.935 0.365
$atom:C1 $mol:m @atom:c3 -0.1264 -4.887 2.427 0.745
$atom:C2 $mol:m @atom:c3 -0.0834 -3.526 2.877 1.311
$atom:C3 $mol:m @atom:c3 0.0697 -2.412 2.743 0.254
$atom:C4 $mol:m @atom:c 0.6131 -1.107 3.318 0.836
$atom:N $mol:m @atom:n -0.5479 -2.202 1.302 -0.147
$atom:C5 $mol:m @atom:c 0.6161 -1.676 0.303 0.856
$atom:C6 $mol:m @atom:c3 0.1095 -1.346 -1.134 0.409
$atom:C7 $mol:m @atom:c3 -0.0152 -0.016 -1.577 1.045
$atom:C8 $mol:m @atom:cc -0.1614 1.103 -0.627 0.581
$atom:O1 $mol:m @atom:o -0.545 -4.341 -0.083 1.352
$atom:O2 $mol:m @atom:o -0.6101 -1.395 0.732 2.276
$atom:N1 $mol:m @atom:n3 -0.8858 -2.45 -2.068 0.845
$atom:C9 $mol:m @atom:ca -0.1038 2.452 -0.392 1.273
$atom:C10 $mol:m @atom:ca -0.0482 3.181 0.709 0.529
$atom:N2 $mol:m @atom:na -0.1904 2.311 1.184 -0.614
$atom:C11 $mol:m @atom:cd -0.0931 1.026 0.375 -0.592
$atom:C12 $mol:m @atom:ca -0.145 4.57 1.189 0.964
$atom:C13 $mol:m @atom:ca -0.111 5.214 0.509 2.197
$atom:C14 $mol:m @atom:ca -0.156 4.463 -0.62 2.961
$atom:C15 $mol:m @atom:ca -0.097 3.059 -1.082 2.499
$atom:O3 $mol:m @atom:oh -0.6061 -1.072 4.742 1.337
$atom:O4 $mol:m @atom:o -0.553 0.136 2.464 0.907
$atom:H $mol:m @atom:ho 0.443 -6.371 0.273 -1.014
$atom:H1 $mol:m @atom:hc 0.0802 -5.691 2.593 1.536
$atom:H2 $mol:m @atom:hc 0.0802 -5.133 3.05 -0.177
$atom:H3 $mol:m @atom:hc 0.0922 -3.262 2.253 2.228
$atom:H4 $mol:m @atom:hc 0.0922 -3.605 3.974 1.612
$atom:H5 $mol:m @atom:h1 0.0987 -2.7 3.351 -0.666
$atom:H6 $mol:m @atom:hn 0.3315 -2.407 0.982 -1.19
$atom:H7 $mol:m @atom:h1 0.0847 -1.249 -1.164 -0.726
$atom:H8 $mol:m @atom:hc 0.0712 0.228 -2.64 0.713
$atom:H9 $mol:m @atom:hc 0.0712 -0.102 -1.541 2.182
$atom:H10 $mol:m @atom:hn 0.3618 -3.406 -1.752 0.379
$atom:H11 $mol:m @atom:hn 0.3618 -2.547 -2.032 1.95
$atom:H12 $mol:m @atom:hn 0.3007 2.562 1.991 -1.333
$atom:H13 $mol:m @atom:h4 0.173 0.143 0.503 -1.301
$atom:H14 $mol:m @atom:ha 0.133 5.11 2.02 0.4
$atom:H15 $mol:m @atom:ha 0.131 6.248 0.837 2.549
$atom:H16 $mol:m @atom:ha 0.133 4.949 -1.111 3.868
$atom:H17 $mol:m @atom:ha 0.158 2.498 -1.908 3.049
$atom:H18 $mol:m @atom:ho 0.448 -0.05 4.983 1.695
} # Atoms section
# bondId atomId1 atomId2
write("Data Bond List") {
$bond:b1 $atom:O $atom:C
$bond:b2 $atom:C $atom:C1
$bond:b3 $atom:C1 $atom:C2
$bond:b4 $atom:C2 $atom:C3
$bond:b5 $atom:C3 $atom:C4
$bond:b6 $atom:C3 $atom:N
$bond:b7 $atom:N $atom:C5
$bond:b8 $atom:C5 $atom:C6
$bond:b9 $atom:C6 $atom:C7
$bond:b10 $atom:C7 $atom:C8
$bond:b11 $atom:C $atom:O1
$bond:b12 $atom:C5 $atom:O2
$bond:b13 $atom:C6 $atom:N1
$bond:b14 $atom:C8 $atom:C9
$bond:b15 $atom:C9 $atom:C10
$bond:b16 $atom:C10 $atom:N2
$bond:b17 $atom:N2 $atom:C11
$bond:b18 $atom:C8 $atom:C11
$bond:b19 $atom:C10 $atom:C12
$bond:b20 $atom:C12 $atom:C13
$bond:b21 $atom:C13 $atom:C14
$bond:b22 $atom:C14 $atom:C15
$bond:b23 $atom:C9 $atom:C15
$bond:b24 $atom:C4 $atom:O3
$bond:b25 $atom:C4 $atom:O4
$bond:b26 $atom:O $atom:H
$bond:b27 $atom:C1 $atom:H1
$bond:b28 $atom:C1 $atom:H2
$bond:b29 $atom:C2 $atom:H3
$bond:b30 $atom:C2 $atom:H4
$bond:b31 $atom:C3 $atom:H5
$bond:b32 $atom:N $atom:H6
$bond:b33 $atom:C6 $atom:H7
$bond:b34 $atom:C7 $atom:H8
$bond:b35 $atom:C7 $atom:H9
$bond:b36 $atom:N1 $atom:H10
$bond:b37 $atom:N1 $atom:H11
$bond:b38 $atom:N2 $atom:H12
$bond:b39 $atom:C11 $atom:H13
$bond:b40 $atom:C12 $atom:H14
$bond:b41 $atom:C13 $atom:H15
$bond:b42 $atom:C14 $atom:H16
$bond:b43 $atom:C15 $atom:H17
$bond:b44 $atom:O3 $atom:H18
} # Bonds section
} # glu
# -------- INSTRUCTIONS FOR USING THIS FILE: --------
# So far, we have just defined (one or more) molecular subunits.
# If you want to use these molecule(s) in a simulation, you must instantiate
# copies of them. To do that you would the "new" command. For example:
#
# glu_instance = new glu
#
# You could either put this command here, or in a separate file.
# (...Such as "system.lt". In that case remember to use moltemplate's
# "import" command to import this file beforehand because you must ensure
# that the molecules in this file are loaded before they are used.)
#
# Note: You can also modify the position and orientation of each copy
# using the .move() and .rot() commands. (See the moltemplate manual.)
# ---------------------------------------------------