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updated hexamer example to use newest topology files
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@tlfobe
tlfobe committed Nov 15, 2022
1 parent be01e6a commit ef8249d
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9 changes: 9 additions & 0 deletions cg_pyrosetta/parameters.py
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Original file line number Diff line number Diff line change
Expand Up @@ -685,8 +685,16 @@ def write_param_file(self, param_filename, structure_file, nbr_radius = 20):
# Find 2 more heavy atoms bonded to

for atom_2 in self.get_neighbors(start_atoms[0]):
print("atom 2 selection")
if self.is_hydrogen(self.atoms[atom_2-1]):
continue
if len(self.get_neighbors(atom_2)) == 1:
continue
h_neighbors = []
for neighbors in self.get_neighbors(atom_2):
h_neighbors.append(self.is_hydrogen(self.atoms[neighbors-1]))
if all(h_neighbors):
continue
else:
start_atoms.append(atom_2)
break
Expand All @@ -702,6 +710,7 @@ def write_param_file(self, param_filename, structure_file, nbr_radius = 20):
continue

# Z-matrix entry 1
print(start_atoms)
z_entry = ["ICOOR_INTERNAL",
self.atoms[start_atoms[0]-1]["atom"],
0,
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288 changes: 288 additions & 0 deletions simulations/terphenyl/mop/hexamer/em_hexamer.gro
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Original file line number Diff line number Diff line change
@@ -0,0 +1,288 @@
System name
285
1HEX C1 1 4.486 4.627 4.312
1HEX O1 2 4.376 4.591 4.268
1HEX C2 3 4.520 4.770 4.305
1HEX C3 4 4.640 4.818 4.362
1HEX C4 5 4.672 4.954 4.357
1HEX C5 6 4.586 5.048 4.297
1HEX C6 7 4.616 5.193 4.298
1HEX C7 8 4.742 5.250 4.265
1HEX C8 9 4.757 5.390 4.275
1HEX C9 10 4.654 5.474 4.316
1HEX O2 11 4.683 5.609 4.322
1HEX C10 12 4.587 5.696 4.381
1HEX C11 13 4.531 5.417 4.347
1HEX C12 14 4.512 5.279 4.338
1HEX C13 15 4.861 5.173 4.220
1HEX C14 16 4.851 5.071 4.124
1HEX C15 17 4.964 5.000 4.084
1HEX C16 18 5.090 5.031 4.137
1HEX C17 19 5.103 5.135 4.230
1HEX C18 20 4.988 5.204 4.271
1HEX C19 21 5.238 5.171 4.290
1HEX N1 22 5.284 5.060 4.374
1HEX C20 23 5.337 5.219 4.184
1HEX C21 24 4.467 5.000 4.241
1HEX C22 25 4.434 4.864 4.244
1HEX H1 26 4.709 4.750 4.411
1HEX H2 27 4.765 4.988 4.402
1HEX H3 28 4.852 5.436 4.249
1HEX H4 29 4.628 5.797 4.387
1HEX H5 30 4.561 5.664 4.482
1HEX H6 31 4.496 5.700 4.320
1HEX H7 32 4.447 5.478 4.379
1HEX H8 33 4.415 5.238 4.366
1HEX H9 34 4.754 5.046 4.081
1HEX H10 35 4.955 4.920 4.011
1HEX H11 36 5.177 4.975 4.104
1HEX H12 37 4.998 5.283 4.344
1HEX H13 38 5.224 5.256 4.358
1HEX H14 39 5.255 5.062 4.471
1HEX H15 40 5.348 5.147 4.103
1HEX H16 41 5.435 5.236 4.229
1HEX H17 42 5.302 5.314 4.141
1HEX H18 43 4.398 5.069 4.192
1HEX H19 44 4.341 4.831 4.199
2HEX C23 45 5.357 4.948 4.338
2HEX O3 46 5.409 4.936 4.228
2HEX C24 47 5.370 4.840 4.437
2HEX C25 48 5.267 4.815 4.529
2HEX C26 49 5.281 4.715 4.625
2HEX C27 50 5.396 4.637 4.634
2HEX C28 51 5.415 4.538 4.743
2HEX C29 52 5.313 4.452 4.794
2HEX C30 53 5.343 4.370 4.904
2HEX C31 54 5.468 4.368 4.965
2HEX O4 55 5.483 4.282 5.071
2HEX C32 56 5.612 4.273 5.133
2HEX C33 57 5.567 4.452 4.914
2HEX C34 58 5.541 4.535 4.806
2HEX C35 59 5.176 4.441 4.738
2HEX C36 60 5.154 4.431 4.600
2HEX C37 61 5.024 4.423 4.549
2HEX C38 62 4.914 4.421 4.635
2HEX C39 63 4.933 4.428 4.774
2HEX C40 64 5.064 4.439 4.823
2HEX C41 65 4.816 4.425 4.871
2HEX N2 66 4.749 4.555 4.876
2HEX C42 67 4.721 4.307 4.848
2HEX C43 68 5.498 4.659 4.538
2HEX C44 69 5.484 4.758 4.441
2HEX H20 70 5.175 4.873 4.526
2HEX H21 71 5.199 4.698 4.694
2HEX H22 72 5.267 4.302 4.943
2HEX H23 73 5.608 4.199 5.214
2HEX H24 74 5.641 4.369 5.177
2HEX H25 75 5.688 4.241 5.061
2HEX H26 76 5.666 4.456 4.958
2HEX H27 77 5.620 4.602 4.772
2HEX H28 78 5.238 4.430 4.531
2HEX H29 79 5.008 4.417 4.441
2HEX H30 80 4.814 4.415 4.593
2HEX H31 81 5.080 4.448 4.931
2HEX H32 82 4.857 4.409 4.972
2HEX H33 83 4.764 4.610 4.961
2HEX H34 84 4.681 4.306 4.747
2HEX H35 85 4.638 4.311 4.919
2HEX H36 86 4.775 4.213 4.864
2HEX H37 87 5.588 4.598 4.539
2HEX H38 88 5.564 4.774 4.368
3HEX C45 89 4.661 4.610 4.784
3HEX O5 90 4.619 4.542 4.691
3HEX C46 91 4.620 4.751 4.796
3HEX C47 92 4.685 4.840 4.883
3HEX C48 93 4.647 4.975 4.890
3HEX C49 94 4.544 5.025 4.809
3HEX C50 95 4.502 5.166 4.815
3HEX C51 96 4.583 5.276 4.777
3HEX C52 97 4.527 5.405 4.789
3HEX C53 98 4.400 5.429 4.839
3HEX O6 99 4.360 5.560 4.847
3HEX C54 100 4.241 5.590 4.922
3HEX C55 101 4.322 5.319 4.877
3HEX C56 102 4.372 5.189 4.864
3HEX C57 103 4.722 5.265 4.724
3HEX C58 104 4.762 5.161 4.640
3HEX C59 105 4.893 5.152 4.594
3HEX C60 106 4.986 5.249 4.628
3HEX C61 107 4.950 5.357 4.710
3HEX C62 108 4.818 5.363 4.757
3HEX C63 109 5.050 5.465 4.748
3HEX N3 110 5.160 5.406 4.825
3HEX C64 111 5.093 5.547 4.626
3HEX C65 112 4.478 4.936 4.723
3HEX C66 113 4.516 4.802 4.715
3HEX H39 114 4.766 4.807 4.947
3HEX H40 115 4.699 5.041 4.958
3HEX H41 116 4.584 5.492 4.758
3HEX H42 117 4.229 5.698 4.929
3HEX H43 118 4.247 5.549 5.023
3HEX H44 119 4.152 5.549 4.872
3HEX H45 120 4.221 5.331 4.916
3HEX H46 121 4.310 5.105 4.894
3HEX H47 122 4.690 5.086 4.608
3HEX H48 123 4.923 5.069 4.530
3HEX H49 124 5.087 5.241 4.589
3HEX H50 125 4.791 5.445 4.823
3HEX H51 126 5.001 5.536 4.816
3HEX H52 127 5.148 5.405 4.926
3HEX H53 128 5.129 5.484 4.544
3HEX H54 129 5.172 5.617 4.653
3HEX H55 130 5.007 5.604 4.588
3HEX H56 131 4.398 4.973 4.659
3HEX H57 132 4.464 4.736 4.646
4HEX C67 133 5.271 5.337 4.777
4HEX O7 134 5.302 5.341 4.659
4HEX C68 135 5.344 5.246 4.867
4HEX C69 136 5.286 5.195 4.984
4HEX C70 137 5.352 5.101 5.063
4HEX C71 138 5.480 5.054 5.028
4HEX C72 139 5.550 4.951 5.107
4HEX C73 140 5.493 4.826 5.145
4HEX C74 141 5.571 4.738 5.222
4HEX C75 142 5.701 4.768 5.264
4HEX O8 143 5.765 4.674 5.340
4HEX C76 144 5.887 4.712 5.406
4HEX C77 145 5.755 4.892 5.226
4HEX C78 146 5.681 4.981 5.148
4HEX C79 147 5.355 4.783 5.109
4HEX C80 148 5.300 4.807 4.982
4HEX C81 149 5.167 4.775 4.955
4HEX C82 150 5.089 4.712 5.051
4HEX C83 151 5.141 4.683 5.177
4HEX C84 152 5.275 4.718 5.204
4HEX C85 153 5.056 4.620 5.286
4HEX N4 154 4.941 4.706 5.316
4HEX C86 155 5.021 4.474 5.253
4HEX C87 156 5.540 5.107 4.912
4HEX C88 157 5.473 5.200 4.833
4HEX H58 158 5.185 5.225 5.014
4HEX H59 159 5.302 5.061 5.150
4HEX H60 160 5.532 4.641 5.251
4HEX H61 161 5.920 4.631 5.472
4HEX H62 162 5.871 4.802 5.467
4HEX H63 163 5.966 4.731 5.333
4HEX H64 164 5.855 4.921 5.255
4HEX H65 165 5.725 5.076 5.122
4HEX H66 166 5.360 4.853 4.904
4HEX H67 167 5.123 4.800 4.859
4HEX H68 168 4.987 4.686 5.024
4HEX H69 169 5.315 4.698 5.303
4HEX H70 170 5.115 4.615 5.378
4HEX H71 171 4.953 4.770 5.393
4HEX H72 172 4.972 4.465 5.156
4HEX H73 173 4.953 4.434 5.330
4HEX H74 174 5.112 4.413 5.252
4HEX H75 175 5.638 5.072 4.882
4HEX H76 176 5.521 5.236 4.742
5HEX C89 177 4.820 4.716 5.250
5HEX O9 178 4.790 4.641 5.157
5HEX C90 179 4.725 4.822 5.289
5HEX C91 180 4.766 4.935 5.362
5HEX C92 181 4.676 5.037 5.394
5HEX C93 182 4.542 5.029 5.354
5HEX C94 183 4.447 5.138 5.384
5HEX C95 184 4.471 5.274 5.351
5HEX C96 185 4.375 5.370 5.387
5HEX C97 186 4.257 5.336 5.453
5HEX O10 187 4.171 5.440 5.480
5HEX C98 188 4.044 5.409 5.540
5HEX C99 189 4.234 5.202 5.484
5HEX C100 190 4.328 5.104 5.450
5HEX C101 191 4.590 5.320 5.274
5HEX C102 192 4.630 5.253 5.158
5HEX C103 193 4.741 5.295 5.086
5HEX C104 194 4.811 5.408 5.126
5HEX C105 195 4.773 5.479 5.240
5HEX C106 196 4.662 5.434 5.314
5HEX C107 197 4.851 5.602 5.285
5HEX N5 198 4.986 5.563 5.327
5HEX C108 199 4.845 5.714 5.181
5HEX C109 200 4.500 4.916 5.283
5HEX C110 201 4.590 4.815 5.250
5HEX H77 202 4.870 4.947 5.393
5HEX H78 203 4.710 5.124 5.450
5HEX H79 204 4.391 5.474 5.361
5HEX H80 205 3.986 5.501 5.553
5HEX H81 206 4.058 5.363 5.639
5HEX H82 207 3.987 5.341 5.477
5HEX H83 208 4.144 5.170 5.535
5HEX H84 209 4.309 5.001 5.476
5HEX H85 210 4.574 5.166 5.123
5HEX H86 211 4.773 5.241 4.998
5HEX H87 212 4.896 5.440 5.066
5HEX H88 213 4.632 5.487 5.404
5HEX H89 214 4.802 5.642 5.374
5HEX H90 215 4.996 5.537 5.424
5HEX H91 216 4.880 5.681 5.082
5HEX H92 217 4.908 5.798 5.213
5HEX H93 218 4.742 5.750 5.170
5HEX H94 219 4.396 4.909 5.250
5HEX H95 220 4.554 4.730 5.192
6HEX C111 221 5.098 5.540 5.249
6HEX O11 222 5.099 5.564 5.128
6HEX C112 223 5.218 5.479 5.310
6HEX C113 224 5.214 5.422 5.439
6HEX C114 225 5.328 5.364 5.496
6HEX C115 226 5.450 5.361 5.426
6HEX C116 227 5.570 5.301 5.487
6HEX C117 228 5.572 5.172 5.547
6HEX C118 229 5.691 5.127 5.608
6HEX C119 230 5.806 5.205 5.612
6HEX O12 231 5.915 5.150 5.676
6HEX C120 232 6.031 5.233 5.695
6HEX C121 233 5.804 5.331 5.551
6HEX C122 234 5.687 5.378 5.490
6HEX C123 235 5.457 5.079 5.545
6HEX C124 236 5.388 5.054 5.426
6HEX C125 237 5.279 4.967 5.423
6HEX C126 238 5.240 4.901 5.539
6HEX C127 239 5.306 4.924 5.660
6HEX C128 240 5.415 5.014 5.662
6HEX C129 241 5.264 4.855 5.788
6HEX N6 242 5.118 4.857 5.802
6HEX C130 243 5.331 4.718 5.799
6HEX C131 244 5.455 5.417 5.298
6HEX C132 245 5.341 5.476 5.241
6HEX H96 246 5.122 5.419 5.497
6HEX H97 247 5.323 5.321 5.595
6HEX H98 248 5.694 5.029 5.653
6HEX H99 249 6.106 5.178 5.753
6HEX H100 250 6.005 5.324 5.750
6HEX H101 251 6.076 5.261 5.599
6HEX H102 252 5.891 5.396 5.551
6HEX H103 253 5.687 5.477 5.445
6HEX H104 254 5.421 5.103 5.334
6HEX H105 255 5.226 4.949 5.330
6HEX H106 256 5.157 4.831 5.535
6HEX H107 257 5.467 5.032 5.755
6HEX H108 258 5.302 4.913 5.873
6HEX H109 259 5.076 4.948 5.819
6HEX H110 260 5.312 4.658 5.709
6HEX H111 261 5.293 4.664 5.886
6HEX H112 262 5.439 4.729 5.809
6HEX H113 263 5.547 5.416 5.241
6HEX H114 264 5.349 5.519 5.141
7CAP C133 265 4.531 4.412 4.400
7CAP O13 266 4.579 4.543 4.364
7CAP H115 267 4.447 4.420 4.471
7CAP H116 268 4.611 4.356 4.449
7CAP H117 269 4.498 4.357 4.312
8CAP C134 270 4.663 4.820 5.755
8CAP C135 271 4.784 4.726 5.760
8CAP C136 272 4.779 4.645 5.890
8CAP C137 273 4.775 4.632 5.639
8CAP O14 274 4.899 4.814 5.759
8CAP C138 275 5.025 4.763 5.763
8CAP O15 276 5.058 4.651 5.730
8CAP H118 277 4.570 4.763 5.760
8CAP H119 278 4.666 4.890 5.839
8CAP H120 279 4.664 4.877 5.662
8CAP H121 280 4.787 4.712 5.977
8CAP H122 281 4.862 4.573 5.895
8CAP H123 282 4.685 4.590 5.898
8CAP H124 283 4.793 4.687 5.546
8CAP H125 284 4.848 4.550 5.645
8CAP H126 285 4.676 4.586 5.633
10.00000 10.00000 10.00000
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