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fix example POPC
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@fgrunewald
fgrunewald committed May 9, 2022
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152 changes: 137 additions & 15 deletions examples/POPC_CHARMM36/POPC.gro
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Original file line number Diff line number Diff line change
@@ -1,15 +1,137 @@
Written by MDAnalysis
12
0POPC NC3 1 7.381 4.404 9.545
0POPC PO4 2 7.504 4.560 9.289
0POPC GL1 3 7.634 4.682 8.999
0POPC GL2 4 7.582 4.493 8.880
0POPC C1A 5 7.607 4.881 8.739
0POPC D2A 6 7.387 5.019 8.244
0POPC C3A 7 7.278 5.190 8.240
0POPC C4A 8 7.348 5.340 8.628
0POPC C1B 9 7.299 4.371 8.520
0POPC C2B 10 7.159 4.414 8.118
0POPC C3B 11 6.948 4.396 7.707
0POPC C4B 12 6.753 4.224 7.484
9.72904 9.72904 15.22278
Title
134
1POPC N 1 4.411 4.636 7.050 -0.0392 0.4733 -0.0553
1POPC C12 2 4.414 4.481 7.053 -0.3342 -0.4702 -0.3511
1POPC H12A 3 4.323 4.449 7.101 -0.3986 -0.7783 -0.6707
1POPC H12B 4 4.502 4.446 7.105 0.6065 -1.4367 -2.4490
1POPC C13 5 4.391 4.696 7.182 0.3777 -0.1307 -0.1521
1POPC H13A 6 4.455 4.648 7.255 0.1012 -0.5856 -0.2025
1POPC H13B 7 4.410 4.802 7.177 -1.3980 0.3100 1.4327
1POPC H13C 8 4.290 4.686 7.219 -0.0954 1.6367 -0.8868
1POPC C14 9 4.549 4.674 6.991 -0.7797 0.0712 0.2984
1POPC H14A 10 4.629 4.647 7.058 -0.8994 -0.6080 0.1702
1POPC H14B 11 4.572 4.630 6.895 0.2797 -0.1725 0.6540
1POPC H14C 12 4.545 4.782 6.984 -2.3384 -0.0492 -1.7052
1POPC C15 13 4.308 4.692 6.956 -1.0741 -0.8192 -0.2449
1POPC H15A 14 4.216 4.650 6.996 -0.4365 -1.7065 0.3178
1POPC H15B 15 4.305 4.644 6.859 -0.9146 -0.6365 -0.3394
1POPC H15C 16 4.299 4.799 6.965 3.1234 -0.4953 2.9043
1POPC C11 17 4.419 4.394 6.919 -0.0504 0.4102 0.3848
1POPC H11A 18 4.431 4.284 6.931 1.5347 0.5496 0.1893
1POPC H11B 19 4.515 4.419 6.869 -0.1012 -0.9925 -0.4606
1POPC P 20 4.159 4.379 6.850 -0.1816 0.4297 -0.1149
1POPC O13 21 4.075 4.489 6.890 -0.3660 0.3235 -0.1364
1POPC O14 22 4.153 4.262 6.932 -0.7790 0.0151 -0.4857
1POPC O12 23 4.307 4.420 6.834 -1.0297 -0.0706 0.0647
1POPC O11 24 4.128 4.330 6.706 0.6939 -0.9511 0.1684
1POPC C1 25 4.188 4.209 6.657 -0.8821 -0.0380 0.5683
1POPC HA 26 4.104 4.153 6.610 -0.7904 -0.3988 0.8340
1POPC HB 27 4.226 4.137 6.732 0.5115 0.0175 -0.0613
1POPC C2 28 4.291 4.234 6.547 -0.8296 0.1559 0.8675
1POPC HS 29 4.360 4.305 6.596 -1.1683 2.1632 -1.3275
1POPC O21 30 4.220 4.305 6.439 -0.1569 0.0651 0.1398
1POPC C21 31 4.285 4.401 6.371 -0.7278 -0.4271 -0.3093
1POPC O22 32 4.397 4.440 6.397 0.3197 -0.8799 -0.2163
1POPC C22 33 4.205 4.461 6.252 -0.1209 -0.8044 0.2030
1POPC H2R 34 4.250 4.556 6.216 1.7759 -1.3587 0.9653
1POPC H2S 35 4.096 4.470 6.273 -0.0699 0.2228 0.0796
1POPC C3 36 4.366 4.114 6.486 -0.1330 0.2158 0.4748
1POPC HX 37 4.426 4.069 6.567 0.5894 0.9149 0.3360
1POPC HY 38 4.433 4.157 6.408 -2.3664 3.1555 0.0118
1POPC O31 39 4.286 4.012 6.420 -0.3268 0.0248 -0.5054
1POPC C31 40 4.221 3.924 6.493 -0.5077 -0.4323 0.2096
1POPC O32 41 4.216 3.916 6.615 0.4261 0.4869 -0.6621
1POPC C32 42 4.149 3.825 6.399 -0.0829 0.0938 0.2449
1POPC H2X 43 4.046 3.803 6.434 0.2245 -2.2297 -0.1143
1POPC H2Y 44 4.200 3.726 6.397 1.8131 0.9530 -3.3792
1POPC C23 45 4.204 4.363 6.136 0.1253 0.3072 -0.1524
1POPC H3R 46 4.114 4.387 6.075 -0.0502 -0.8896 -0.3931
1POPC H3S 47 4.195 4.254 6.157 1.7751 -0.3941 -2.6143
1POPC C24 48 4.321 4.373 6.038 0.3218 -0.5529 0.1883
1POPC H4R 49 4.420 4.362 6.088 0.1454 -0.8297 0.4796
1POPC H4S 50 4.311 4.473 5.991 0.7928 0.4161 2.0726
1POPC C25 51 4.298 4.261 5.933 0.3008 0.7821 -0.3163
1POPC H5R 52 4.189 4.258 5.912 0.4901 -0.6764 -1.2226
1POPC H5S 53 4.309 4.161 5.979 -0.5507 1.9614 2.6647
1POPC C26 54 4.380 4.285 5.810 0.7081 0.2074 -0.7546
1POPC H6R 55 4.484 4.301 5.844 1.0076 -0.8247 -1.1479
1POPC H6S 56 4.342 4.378 5.764 -1.8665 -0.6464 -0.5520
1POPC C27 57 4.379 4.166 5.710 0.4910 -0.2946 0.2641
1POPC H7R 58 4.270 4.154 5.693 0.3895 -0.8874 1.2479
1POPC H7S 59 4.411 4.072 5.759 0.4406 -0.4232 0.0515
1POPC C28 60 4.462 4.187 5.580 -0.2606 -0.1670 0.0276
1POPC H8R 61 4.571 4.176 5.602 0.4629 -3.7755 -3.9697
1POPC H8S 62 4.451 4.290 5.541 -2.6927 -0.0459 0.8718
1POPC C29 63 4.425 4.072 5.491 0.0324 -0.6214 -0.2382
1POPC H91 64 4.400 3.978 5.541 0.0404 -0.0779 0.8355
1POPC C210 65 4.433 4.080 5.357 0.0534 -0.2013 -0.1123
1POPC H101 66 4.401 3.997 5.292 -0.0826 0.3847 -0.8050
1POPC C211 67 4.470 4.204 5.277 -0.4903 -0.0175 -0.1766
1POPC H11R 68 4.544 4.182 5.197 -2.2447 -0.5178 -1.7293
1POPC H11S 69 4.512 4.280 5.346 -2.7869 -0.0456 1.3522
1POPC C212 70 4.335 4.257 5.214 0.0320 -0.4837 0.6926
1POPC H12R 71 4.355 4.344 5.148 2.8366 -1.1588 0.4962
1POPC H12S 72 4.263 4.290 5.291 -1.8495 -3.3391 0.3214
1POPC C213 73 4.274 4.152 5.120 0.0175 0.6689 -0.2502
1POPC H13R 74 4.186 4.202 5.073 -0.5601 -2.4755 -2.8430
1POPC H13S 75 4.242 4.058 5.170 -1.2503 -0.5058 -3.0407
1POPC C214 76 4.368 4.101 4.997 -0.4770 -1.1569 -0.2889
1POPC H14R 77 4.451 4.048 5.049 -1.1756 0.6386 2.9560
1POPC H14S 78 4.419 4.192 4.959 -0.4530 -1.0702 -0.0518
1POPC C215 79 4.295 4.025 4.889 0.5896 -0.4700 0.0384
1POPC H15R 80 4.252 4.100 4.819 -0.2689 -0.4391 0.5745
1POPC H15S 81 4.203 3.980 4.934 1.5154 -2.0108 0.4604
1POPC C216 82 4.387 3.922 4.818 0.1536 -0.3975 0.2348
1POPC H16R 83 4.354 3.828 4.868 -1.4023 -0.2546 -0.4307
1POPC H16S 84 4.494 3.936 4.843 0.6662 -0.1387 -1.9082
1POPC C217 85 4.357 3.913 4.671 -0.5637 0.1826 0.0528
1POPC H17R 86 4.366 4.019 4.641 0.8617 0.8163 2.4733
1POPC H17S 87 4.255 3.869 4.662 -0.6163 0.2983 0.0875
1POPC C218 88 4.454 3.821 4.594 0.0333 0.1947 -0.0416
1POPC H18R 89 4.559 3.844 4.622 -0.3004 1.2457 0.3679
1POPC H18S 90 4.441 3.856 4.490 0.7587 -0.2746 -0.2981
1POPC H18T 91 4.422 3.717 4.616 -1.1090 0.6290 0.4248
1POPC C33 92 4.140 3.869 6.247 -0.4625 -0.0650 0.2183
1POPC H3X 93 4.116 3.777 6.188 0.4995 0.1748 -0.5782
1POPC H3Y 94 4.237 3.894 6.198 -1.6084 0.0782 -2.1372
1POPC C34 95 4.040 3.983 6.222 0.1777 0.4315 -0.3776
1POPC H4X 96 4.076 4.066 6.287 -0.2682 1.5240 -1.4946
1POPC H4Y 97 3.937 3.953 6.252 0.5068 -0.6388 -0.2595
1POPC C35 98 4.036 4.035 6.082 -0.5710 0.4161 0.0304
1POPC H5X 99 4.140 4.065 6.058 0.6322 -3.2158 0.0592
1POPC H5Y 100 3.976 4.128 6.069 1.0857 1.6133 0.6311
1POPC C36 101 3.995 3.929 5.976 -0.2654 0.0048 -0.0526
1POPC H6X 102 3.887 3.911 5.994 -0.5605 1.1052 -0.6527
1POPC H6Y 103 4.057 3.844 6.012 0.1108 0.4895 0.4643
1POPC C37 104 4.027 3.960 5.829 0.1923 -1.0921 0.5292
1POPC H7X 105 4.012 3.870 5.766 0.3294 0.2825 -1.5732
1POPC H7Y 106 4.133 3.992 5.822 -0.5150 1.1962 -0.7684
1POPC C38 107 3.930 4.069 5.776 -0.3812 0.4071 -0.0445
1POPC H8X 108 3.926 4.154 5.848 0.6566 2.1353 -1.9319
1POPC H8Y 109 3.831 4.022 5.763 1.0079 -2.1703 -2.2466
1POPC C39 110 3.963 4.138 5.642 0.0003 -0.1036 0.0311
1POPC H9X 111 3.964 4.073 5.552 -1.3383 1.8769 -1.4931
1POPC H9Y 112 4.058 4.193 5.658 1.3207 -2.1420 -0.3711
1POPC C310 113 3.858 4.245 5.618 -0.2324 -0.5475 0.6030
1POPC H10X 114 3.865 4.326 5.694 1.1953 -0.4047 0.3588
1POPC H10Y 115 3.754 4.208 5.624 -0.5807 0.3467 0.2557
1POPC C311 116 3.867 4.304 5.467 0.7182 0.0378 0.2088
1POPC H11X 117 3.792 4.386 5.470 1.3471 0.6179 0.2095
1POPC H11Y 118 3.821 4.235 5.392 -0.5158 0.9058 0.1239
1POPC C312 119 3.995 4.371 5.424 0.7236 0.2699 -0.4311
1POPC H12X 120 3.971 4.403 5.321 0.4900 -0.7743 -0.7090
1POPC H12Y 121 4.086 4.308 5.433 0.6565 0.0032 -1.5103
1POPC C313 122 4.013 4.499 5.509 0.4294 -0.2209 -0.6973
1POPC H13X 123 4.005 4.477 5.618 5.2383 0.2236 -0.0542
1POPC H13Y 124 3.938 4.578 5.484 2.4595 2.3596 0.7991
1POPC C314 125 4.153 4.564 5.485 -0.0491 0.1871 0.2139
1POPC H14X 126 4.234 4.488 5.484 -2.1671 -2.2423 -2.2092
1POPC H14Y 127 4.162 4.623 5.579 -0.1355 -0.9886 0.9827
1POPC C315 128 4.173 4.653 5.363 0.0819 -0.6260 -0.1343
1POPC H15X 129 4.117 4.748 5.375 0.4691 -0.5011 0.8031
1POPC H15Y 130 4.122 4.615 5.272 1.5007 -1.2028 -0.7186
1POPC C316 131 4.318 4.662 5.328 0.7147 0.4874 0.3586
1POPC H16X 132 4.378 4.700 5.413 2.0558 -1.5407 0.3869
1POPC H16Y 133 4.323 4.722 5.234 0.3035 -2.5967 -1.7781
1POPC H16Z 134 4.351 4.557 5.315 1.1358 0.5417 0.9457
7.38272 7.38272 10.36243
15 changes: 15 additions & 0 deletions examples/POPC_CHARMM36/POPC_mapped.gro
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Written by MDAnalysis
12
0POPC NC3 1 4.415 4.594 7.020
0POPC PO4 2 4.304 4.305 6.803
0POPC GL1 3 4.229 4.302 6.484
0POPC GL2 4 4.268 4.033 6.483
0POPC C1A 5 4.251 4.386 6.163
0POPC D2A 6 4.397 4.160 5.603
0POPC C3A 7 4.386 4.105 5.276
0POPC C4A 8 4.356 3.989 4.848
0POPC C1B 9 4.078 3.921 6.207
0POPC C2B 10 3.956 4.087 5.828
0POPC C3B 11 3.983 4.362 5.535
0POPC C4B 12 4.176 4.607 5.420
7.38272 7.38272 10.36243
2 changes: 1 addition & 1 deletion examples/POPC_CHARMM36/commands.txt
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ff_map -f POPC_noH.gro -s POPC_noH.tpr -mf POPC.map -o POPC_mapped_H_re.gro -mols POPC -add_H CTL1:CH1 CTL2:CH2 CTL5:CH3 CEL1:CHd
ff_map -f POPC.gro -s POPC.tpr -mf POPC.map -o POPC.gro -mols POPC
ff_map -f POPC.gro -s POPC.tpr -mf POPC.map -o POPC_mapped.gro -mols POPC

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