unanswered Problem in AA to CG file conversion of RNA strand!

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1 year 9 months ago #8716 by mukhergm
Dear All,

I have a problem of all atom (AA) to CG file conversion of RNA strand.
The following command I used:
python2 martinize-nucleotide.py -type ds-stiff -f Anu10.gro -o cg-1rna.top -x cg-1rna.pdb

Where, Anu10.gro is the AA structure of RNA.

The following error message I got while running the aforementioned command:
Traceback (most recent call last):
File "martinize-nucleotide.py", line 5023, in <module>
main(options)
File "martinize-nucleotide.py", line 4529, in main
order, merge = check_merge(chains, options, options, options and options)
File "martinize-nucleotide.py", line 2720, in check_merge
merges = [[(i.isdigit() and int(i) or dct+1)-1 for i in j] for j in m_list]
KeyError: 'B'

Could you please help me in this regards.

Thanks and Best Regards,
Goutam

Coordinates of Anu10.gro
God Rules Over Mankind, Animals, Cosmos and Such
193
2C P 1 5.841 3.667 6.654
2C C5' 2 5.831 3.916 6.741
2C O5' 3 5.781 3.815 6.653
2C C4' 4 5.791 4.056 6.692
2C O4' 5 5.786 4.149 6.799
2C C3' 6 5.886 4.118 6.589
2C O3' 7 5.851 4.081 6.457
2C C2' 8 5.871 4.269 6.616
2C O2' 9 5.811 4.342 6.510
2C C1' 10 5.777 4.276 6.737
2C N1 11 5.806 4.388 6.831
2C C2 12 5.706 4.483 6.857
2C O2 13 5.592 4.472 6.812
2C N3 14 5.733 4.591 6.935
2C C4 15 5.852 4.604 6.987
2C N4 16 5.872 4.710 7.060
2C C5 17 5.957 4.509 6.968
2C C6 18 5.930 4.402 6.889
2C OP1 19 5.755 3.582 6.568
2C OP2 20 5.985 3.674 6.626
3A P 21 5.958 4.085 6.340
3A C5' 22 6.117 4.293 6.345
3A O5' 23 5.988 4.241 6.316
3A C4' 24 6.137 4.440 6.305
3A O4' 25 6.272 4.476 6.335
3A C3' 26 6.118 4.466 6.155
3A O3' 27 6.088 4.604 6.140
3A C2' 28 6.258 4.429 6.103
3A O2' 29 6.287 4.483 5.975
3A C1' 30 6.343 4.492 6.212
3A N1 31 6.635 4.075 6.311
3A C2 32 6.503 4.092 6.307
3A N3 33 6.437 4.203 6.279
3A C4 34 6.518 4.307 6.248
3A C5 35 6.655 4.305 6.243
3A C6 36 6.711 4.179 6.278
3A N6 37 6.840 4.153 6.283
3A N7 38 6.706 4.430 6.206
3A C8 39 6.599 4.503 6.194
3A N9 40 6.481 4.437 6.217
3A OP1 41 6.081 4.020 6.387
3A OP2 42 5.893 4.032 6.218
4A P 43 6.020 4.664 6.010
4A C5' 44 5.799 4.525 5.978
4A O5' 45 5.865 4.639 6.032
4A C4' 46 5.652 4.522 6.020
4A O4' 47 5.637 4.502 6.160
4A C3' 48 5.579 4.651 5.984
4A O3' 49 5.539 4.648 5.847
4A C2' 50 5.463 4.648 6.084
4A O2' 51 5.352 4.570 6.040
4A C1' 52 5.525 4.578 6.205
4A N1 53 5.360 4.871 6.592
4A C2 54 5.297 4.792 6.507
4A N3 55 5.349 4.721 6.407
4A C4 56 5.484 4.737 6.398
4A C5 57 5.563 4.815 6.478
4A C6 58 5.492 4.883 6.580
4A N6 59 5.545 4.964 6.669
4A N7 60 5.698 4.807 6.437
4A C8 61 5.694 4.723 6.337
4A N9 62 5.568 4.677 6.307
4A OP1 63 6.066 4.585 5.894
4A OP2 64 6.043 4.810 6.009
5U P 65 5.515 4.782 5.766
5U C5' 66 5.255 4.792 5.793
5U O5' 67 5.382 4.844 5.829
5U C4' 68 5.145 4.838 5.889
5U O4' 69 5.184 4.814 6.024
5U C3' 70 5.109 4.986 5.880
5U O3' 71 5.014 5.011 5.777
5U C2' 72 5.043 5.004 6.017
5U O2' 73 4.910 4.955 6.018
5U C1' 74 5.125 4.912 6.109
5U N1 75 5.225 4.990 6.188
5U C2 76 5.183 5.043 6.310
5U O2 77 5.067 5.036 6.350
5U N3 78 5.277 5.107 6.388
5U C4 79 5.409 5.123 6.355
5U O4 80 5.485 5.176 6.434
5U C5 81 5.445 5.072 6.224
5U C6 82 5.355 5.009 6.144
5U OP1 83 5.486 4.742 5.626
5U OP2 84 5.628 4.874 5.790
6U P 85 4.983 5.159 5.725
6U C5' 86 4.802 5.245 5.898
6U O5' 87 4.936 5.246 5.851
6U C4' 88 4.787 5.322 6.030
6U O4' 89 4.875 5.272 6.130
6U C3' 90 4.818 5.471 6.016
6U O3' 91 4.709 5.546 5.963
6U C2' 92 4.854 5.508 6.161
6U O2' 93 4.740 5.544 6.237
6U C1' 94 4.909 5.378 6.219
6U N1 95 5.056 5.388 6.242
6U C2 96 5.100 5.414 6.372
6U O2 97 5.023 5.414 6.468
6U N3 98 5.234 5.441 6.391
6U C4 99 5.328 5.444 6.292
6U O4 100 5.444 5.472 6.319
6U C5 101 5.278 5.412 6.160
6U C6 102 5.146 5.386 6.137
6U OP1 103 4.870 5.147 5.630
6U OP2 104 5.108 5.218 5.674
7A P 105 4.721 5.703 5.944
7A C5' 106 4.536 5.782 6.115
7A O5' 107 4.674 5.759 6.087
7A C4' 108 4.511 5.832 6.258
7A O4' 109 4.543 5.734 6.356
7A C3' 110 4.589 5.957 6.294
7A O3' 111 4.525 6.073 6.242
7A C2' 112 4.589 5.949 6.448
7A O2' 113 4.485 6.026 6.505
7A C1' 114 4.555 5.802 6.480
7A N1 115 4.664 5.659 6.964
7A C2 116 4.558 5.716 6.910
7A N3 117 4.536 5.749 6.782
7A C4 118 4.642 5.716 6.703
7A C5 119 4.758 5.653 6.743
7A C6 120 4.765 5.626 6.882
7A N6 121 4.866 5.568 6.942
7A N7 122 4.842 5.631 6.634
7A C8 123 4.779 5.686 6.534
7A N9 124 4.655 5.737 6.568
7A OP1 125 4.623 5.746 5.841
7A OP2 126 4.863 5.733 5.922
8A P 127 4.602 6.212 6.227
8A C5' 128 4.495 6.363 6.417
8A O5' 129 4.597 6.272 6.377
8A C4' 130 4.494 6.393 6.568
8A O4' 131 4.496 6.272 6.643
8A C3' 132 4.606 6.486 6.621
8A O3' 133 4.552 6.616 6.647
8A C2' 134 4.651 6.416 6.751
8A O2' 135 4.588 6.464 6.868
8A C1' 136 4.604 6.272 6.734
8A N1 137 4.923 5.917 6.918
8A C2 138 4.805 5.961 6.960
8A N3 139 4.722 6.045 6.899
8A C4 140 4.771 6.088 6.779
8A C5 141 4.889 6.050 6.721
8A C6 142 4.966 5.960 6.799
8A N6 143 5.087 5.919 6.766
8A N7 144 4.909 6.115 6.600
8A C8 145 4.806 6.194 6.591
8A N9 146 4.717 6.184 6.696
8A OP1 147 4.520 6.296 6.137
8A OP2 148 4.740 6.182 6.189
9A P 149 4.644 6.743 6.681
9A C5' 150 4.593 6.762 6.940
9A O5' 151 4.683 6.726 6.837
9A C4' 152 4.653 6.740 7.080
9A O4' 153 4.719 6.614 7.092
9A C3' 154 4.755 6.845 7.125
9A O3' 155 4.696 6.957 7.189
9A C2' 156 4.832 6.767 7.232
9A O2' 157 4.759 6.771 7.355
9A C1' 158 4.834 6.626 7.175
9A N1 159 5.335 6.518 7.225
9A C2 160 5.238 6.537 7.313
9A N3 161 5.110 6.568 7.293
9A C4 162 5.083 6.577 7.159
9A C5 163 5.171 6.560 7.056
9A C6 164 5.303 6.531 7.096
9A N6 165 5.405 6.514 7.014
9A N7 166 5.107 6.578 6.932
9A C8 167 4.983 6.603 6.965
9A N9 168 4.960 6.604 7.101
9A OP1 169 4.556 6.861 6.669
9A OP2 170 4.766 6.736 6.601
10G P 171 4.703 7.100 7.124
10G C5' 172 4.945 7.135 7.213
10G O5' 173 4.859 7.121 7.102
10G C4' 174 5.091 7.109 7.176
10G O4' 175 5.116 6.977 7.129
10G C3' 176 5.144 7.198 7.064
10G O3' 177 5.155 7.335 7.100
10G C2' 178 5.278 7.127 7.039
10G O2' 179 5.377 7.159 7.136
10G C1' 180 5.239 6.980 7.056
10G N1 181 5.522 6.796 6.673
10G C2 182 5.557 6.840 6.796
10G N2 183 5.685 6.847 6.823
10G N3 184 5.473 6.880 6.891
10G C4 185 5.342 6.876 6.850
10G C5 186 5.296 6.835 6.727
10G C6 187 5.391 6.788 6.629
10G O6 188 5.374 6.745 6.516
10G N7 189 5.157 6.851 6.721
10G C8 190 5.125 6.899 6.839
10G N9 191 5.232 6.916 6.922
10G OP1 192 4.651 7.194 7.226
10G OP2 193 4.631 7.093 6.996
0.00000 0.00000 0.00000

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