AMBER Archive (2008)

Subject: AMBER: tleap error message

From: Wang,Ying (wangying_at_ufl.edu)
Date: Fri May 30 2008 - 11:08:14 CDT

Hi, dear ambers,

when i load a pdb file by tleap. there is a error message is as
below:

ERROR: Comparing atoms
        .R<0GB 5>.A<C3 15>,
        .R<0GB 5>.A<C1 1>,
        .R<0GB 5>.A<H2 20>, and
        .R<0GB 5>.A<O2 21>
       to atoms
        .R<0GB 5>.A<C3 15>,
        .R<0XA 1>.A<C1 1>,
        .R<0GB 5>.A<H2 20>, and
        .R<0GB 5>.A<C1 1>
       This error may be due to faulty Connection atoms.
!FATAL ERROR----------------------------------------
!FATAL: In file [chirality.c], line 140
!FATAL: Message: Atom named C1 from 0XA did not match !
!
!ABORTING.

this pdb file is four 1-4 link beta d glucose then link three
branch alpha d xylp (1-6)

the pdb file is as below:

REMARK
ATOM 1 1HO ROH 1 94.197 3.673 24.245
ATOM 2 O1 ROH 1 93.543 4.370 24.164
ATOM 3 C1 UGB 2 92.337 3.952 23.615
ATOM 4 H1 UGB 2 92.446 3.640 22.582
ATOM 5 O5 UGB 2 91.894 2.828 24.392
ATOM 6 C5 UGB 2 90.650 2.216 24.059
ATOM 7 H5 UGB 2 90.639 1.932 23.012
ATOM 8 C6 UGB 2 90.536 0.967 24.905
ATOM 9 O6 UGB 2 91.544 0.063 24.419
ATOM 10 1H6 UGB 2 89.563 0.514 24.791
ATOM 11 2H6 UGB 2 90.718 1.201 25.944
ATOM 12 C4 UGB 2 89.566 3.251 24.307
ATOM 13 H4 UGB 2 89.471 3.462 25.366
ATOM 14 C3 UGB 2 89.883 4.537 23.548
ATOM 15 H3 UGB 2 89.725 4.342 22.494
ATOM 16 O3 UGB 2 89.037 5.600 23.984
ATOM 17 H3O UGB 2 88.114 5.449 23.778
ATOM 18 C2 UGB 2 91.309 5.058 23.727
ATOM 19 H2 UGB 2 91.402 5.498 24.711
ATOM 20 O2 UGB 2 91.586 5.997 22.703
ATOM 21 H2O UGB 2 91.145 6.843 22.804
ATOM 22 O4 UGB 2 88.347 2.663 23.811
ATOM 23 C1 UGB 3 87.098 3.023 24.297
ATOM 24 H1 UGB 3 87.125 3.205 25.365
ATOM 25 O5 UGB 3 86.700 4.232 23.626
ATOM 26 C5 UGB 3 85.403 4.769 23.917
ATOM 27 H5 UGB 3 85.307 4.949 24.982
ATOM 28 C6 UGB 3 85.287 6.079 23.177
ATOM 29 O6 UGB 3 86.192 6.999 23.809
ATOM 30 1H6 UGB 3 84.274 6.455 23.242
ATOM 31 2H6 UGB 3 85.564 5.949 22.141
ATOM 32 C4 UGB 3 84.373 3.733 23.490
ATOM 33 H4 UGB 3 84.352 3.634 22.411
ATOM 34 C3 UGB 3 84.670 2.381 24.128
ATOM 35 H3 UGB 3 84.451 2.458 25.187
ATOM 36 O3 UGB 3 83.878 1.356 23.532
ATOM 37 H3O UGB 3 82.940 1.468 23.693
ATOM 38 C2 UGB 3 86.115 1.921 23.964
ATOM 39 H2 UGB 3 86.277 1.627 22.936
ATOM 40 O2 UGB 3 86.386 0.860 24.862
ATOM 41 H2O UGB 3 85.930 0.037 24.671
ATOM 42 O4 UGB 3 83.110 4.240 23.964
ATOM 43 C1 UGB 4 81.902 3.916 23.363
ATOM 44 H1 UGB 4 81.998 3.856 22.285
ATOM 45 O5 UGB 4 81.492 2.634 23.872
ATOM 46 C5 UGB 4 80.208 2.113 23.502
ATOM 47 H5 UGB 4 80.147 2.009 22.425
ATOM 48 C6 UGB 4 80.100 0.749 24.143
ATOM 49 O6 UGB 4 81.031 -0.107 23.468
ATOM 50 1H6 UGB 4 79.097 0.357 24.027
ATOM 51 2H6 UGB 4 80.347 0.808 25.193
ATOM 52 C4 UGB 4 79.150 3.107 23.970
ATOM 53 H4 UGB 4 79.108 3.144 25.052
ATOM 54 C3 UGB 4 79.465 4.489 23.407
ATOM 55 H3 UGB 4 79.370 4.439 22.328
ATOM 56 O3 UGB 4 78.593 5.493 23.916
ATOM 57 H3O UGB 4 77.675 5.220 23.894
ATOM 58 C2 UGB 4 80.871 4.947 23.763
ATOM 59 H2 UGB 4 80.942 5.100 24.832
ATOM 60 O2 UGB 4 81.182 6.138 23.056
ATOM 61 H2O UGB 4 80.573 6.844 23.256
ATOM 62 O4 UGB 4 77.884 2.661 23.442
ATOM 63 C1 0GB 5 76.737 2.672 24.245
ATOM 64 H1 0GB 5 76.918 2.148 25.177
ATOM 65 O5 0GB 5 76.387 4.023 24.526
ATOM 66 C5 0GB 5 75.215 4.226 25.364
ATOM 67 H5 0GB 5 75.361 3.704 26.302
ATOM 68 C6 0GB 5 75.129 5.711 25.633
ATOM 69 1H6 0GB 5 74.257 5.918 26.227
ATOM 70 2H6 0GB 5 75.052 6.250 24.695
ATOM 71 O6 0GB 5 76.251 6.152 26.392
ATOM 72 H6O 0GB 5 77.069 6.157 25.904
ATOM 73 C4 0GB 5 74.029 3.634 24.617
ATOM 74 H4 0GB 5 73.852 4.192 23.705
ATOM 75 O4 0GB 5 72.908 3.725 25.483
ATOM 76 H4O 0GB 5 72.126 3.331 25.107
ATOM 77 C3 0GB 5 74.308 2.183 24.254
ATOM 78 H3 0GB 5 74.383 1.599 25.164
ATOM 79 O3 0GB 5 73.191 1.743 23.489
ATOM 80 H3O 0GB 5 73.244 0.821 23.254
ATOM 81 C2 0GB 5 75.600 2.041 23.469
ATOM 82 H2 0GB 5 75.514 2.551 22.519
ATOM 83 O2 0GB 5 75.815 0.646 23.283
ATOM 84 H2O 0GB 5 76.446 0.446 22.600
ATOM 85 C1 0XA 6 81.071 -1.481 23.836
ATOM 86 H1 0XA 6 80.065 -1.868 23.894
ATOM 87 C2 0XA 6 81.882 -2.199 22.764
ATOM 88 H2 0XA 6 81.732 -3.262 22.873
ATOM 89 O2 0XA 6 81.410 -1.872 21.459
ATOM 90 H2O 0XA 6 81.301 -0.930 21.355
ATOM 91 C3 0XA 6 83.365 -1.893 22.888
ATOM 92 H3 0XA 6 83.560 -0.859 22.640
ATOM 93 O3 0XA 6 84.126 -2.758 22.038
ATOM 94 H3O 0XA 6 83.872 -2.697 21.123
ATOM 95 C4 0XA 6 83.857 -2.161 24.296
ATOM 96 H4 0XA 6 83.789 -3.224 24.492
ATOM 97 O4 0XA 6 85.217 -1.739 24.431
ATOM 98 H4O 0XA 6 85.796 -2.231 23.855
ATOM 99 C5 0XA 6 83.035 -1.390 25.312
ATOM 100 H5A 0XA 6 83.219 -0.334 25.214
ATOM 101 H5E 0XA 6 83.252 -1.707 26.317
ATOM 102 O5 0XA 6 81.626 -1.676 25.114
ATOM 103 C1 0XA 7 86.220 8.341 23.346
ATOM 104 H1 0XA 7 85.212 8.702 23.220
ATOM 105 C2 0XA 7 86.976 9.150 24.393
ATOM 106 H2 0XA 7 86.814 10.200 24.202
ATOM 107 O2 0XA 7 86.460 8.907 25.701
ATOM 108 H2O 0XA 7 86.331 7.975 25.853
ATOM 109 C3 0XA 7 88.468 8.863 24.349
ATOM 110 H3 0XA 7 88.670 7.853 24.676
ATOM 111 O3 0XA 7 89.178 9.800 25.169
ATOM 112 H3O 0XA 7 88.892 9.784 26.077
ATOM 113 C4 0XA 7 89.012 9.044 22.947
ATOM 114 H4 0XA 7 88.929 10.088 22.672
ATOM 115 O4 0XA 7 90.385 8.645 22.892
ATOM 116 H4O 0XA 7 90.925 9.166 23.480
ATOM 117 C5 0XA 7 88.245 8.182 21.960
ATOM 118 H5A 0XA 7 88.440 7.141 22.148
ATOM 119 H5E 0XA 7 88.501 8.425 20.944
ATOM 120 O5 0XA 7 86.826 8.461 22.079
ATOM 121 C1 0XA 8 92.367 -0.719 25.275
ATOM 122 H1 0XA 8 91.800 -1.527 25.705
ATOM 123 C2 0XA 8 93.486 -1.203 24.366
ATOM 124 H2 0XA 8 94.093 -1.927 24.888
ATOM 125 O2 0XA 8 92.971 -1.868 23.213
ATOM 126 H2O 0XA 8 92.205 -1.412 22.872
ATOM 127 C3 0XA 8 94.335 -0.016 23.937
ATOM 128 H3 0XA 8 93.728 0.648 23.338
ATOM 129 O3 0XA 8 95.474 -0.446 23.186
ATOM 130 H3O 0XA 8 95.237 -1.026 22.468
ATOM 131 C4 0XA 8 94.878 0.755 25.123
ATOM 132 H4 0XA 8 95.657 0.162 25.584
ATOM 133 O4 0XA 8 95.428 2.005 24.674
ATOM 134 H4O 0XA 8 96.183 1.876 24.106
ATOM 135 C5 0XA 8 93.794 1.112 26.130
ATOM 136 H5A 0XA 8 93.228 1.950 25.772
ATOM 137 H5E 0XA 8 94.219 1.335 27.093
ATOM 138 O5 0XA 8 92.903 -0.011 26.367
TER
END

could any body tell me the error reason? thanks a lot!!

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