CCL: bondAtomProblem
- From: "amine amine" <m-22##hotmail.fr>
- Subject: CCL: bondAtomProblem
- Date: Tue, 16 Sep 2008 17:14:10 -0400
Sent to CCL by: "amine amine" [m-22||hotmail.fr]
Hi,
This is my pdb file and i recive:
Bond: Maximum coordination exceeded on .R<MOL 1>.A<H10 100>
-- setting atoms pert=true overrides default limits
ATOMS NOT BONDED: .R<MOL 1>.A<C97 97> .R<MOL 1>.A<H10
100>
!FATAL ERROR----------------------------------------
!FATAL: In file [atom.c], line 444
!FATAL: Message: bondAtomProblem found
!
!ABORTING.
when i make loadpdb file.pdb into leap in amber10, What's the wrong
------------------------------------------------------------
ATOM 1 O1 MOL 1 0.483 3.644 -6.151
ATOM 2 H2 MOL 1 0.276 2.895 -6.696
ATOM 3 C3 MOL 1 0.521 3.200 -4.826
ATOM 4 H4 MOL 1 1.164 2.302 -4.726
ATOM 5 H5 MOL 1 1.014 4.038 -4.297
ATOM 6 C6 MOL 1 -0.859 2.900 -4.197
ATOM 7 O7 MOL 1 -1.505 4.168 -4.052
ATOM 8 H8 MOL 1 -0.676 2.470 -3.180
ATOM 9 C9 MOL 1 -1.725 1.910 -5.020
ATOM 10 O10 MOL 1 -1.106 0.628 -4.921
ATOM 11 H11 MOL 1 -1.810 2.237 -6.089
ATOM 12 C12 MOL 1 -3.144 1.783 -4.392
ATOM 13 O13 MOL 1 -4.022 1.056 -5.224
ATOM 14 H14 MOL 1 -3.597 0.222 -5.428
ATOM 15 H15 MOL 1 -3.083 1.278 -3.396
ATOM 16 C16 MOL 1 -3.763 3.196 -4.243
ATOM 17 O17 MOL 1 -4.980 3.190 -3.523
ATOM 18 H18 MOL 1 -5.519 2.506 -3.900
ATOM 19 H19 MOL 1 -3.963 3.633 -5.254
ATOM 20 C20 MOL 1 -2.788 4.146 -3.489
ATOM 21 H21 MOL 1 -3.112 5.214 -3.554
ATOM 22 O22 MOL 1 -2.561 3.717 -2.162
ATOM 23 C23 MOL 1 -2.883 4.658 -1.137
ATOM 24 C24 MOL 1 -1.587 4.924 -0.325
ATOM 25 O25 MOL 1 -1.857 5.671 0.865
ATOM 26 C26 MOL 1 -0.518 5.734 -1.094
ATOM 27 O27 MOL 1 -0.952 6.968 -1.588
ATOM 28 H28 MOL 1 -1.536 6.794 -2.317
ATOM 29 H29 MOL 1 0.312 6.017 -0.420
ATOM 30 H30 MOL 1 -0.103 5.104 -1.907
ATOM 31 H31 MOL 1 -1.124 3.946 -0.040
ATOM 32 H32 MOL 1 -3.288 5.608 -1.572
ATOM 33 C33 MOL 1 -3.960 3.983 -0.239
ATOM 34 O34 MOL 1 -5.215 3.926 -0.882
ATOM 35 H35 MOL 1 -5.077 3.534 -1.746
ATOM 36 H36 MOL 1 -3.643 2.945 0.032
ATOM 37 C37 MOL 1 -4.170 4.832 1.041
ATOM 38 O38 MOL 1 -4.996 4.196 1.996
ATOM 39 H39 MOL 1 -5.755 3.869 1.530
ATOM 40 H40 MOL 1 -4.642 5.811 0.776
ATOM 41 C41 MOL 1 -2.808 5.122 1.736
ATOM 42 H42 MOL 1 -2.901 5.902 2.531
ATOM 43 O43 MOL 1 -2.196 3.935 2.195
ATOM 44 C44 MOL 1 -1.874 3.900 3.585
ATOM 45 C45 MOL 1 -2.675 2.712 4.195
ATOM 46 C46 MOL 1 -2.183 2.455 5.642
ATOM 47 O47 MOL 1 -2.733 1.283 6.208
ATOM 48 H48 MOL 1 -3.668 1.315 6.047
ATOM 49 H49 MOL 1 -2.459 3.317 6.299
ATOM 50 O50 MOL 1 -4.052 3.007 4.291
ATOM 51 H51 MOL 1 -4.343 3.298 3.425
ATOM 52 H52 MOL 1 -2.542 1.793 3.571
ATOM 53 H53 MOL 1 -2.165 4.856 4.092
ATOM 54 C54 MOL 1 -0.349 3.644 3.705
ATOM 55 C55 MOL 1 0.527 4.842 3.267
ATOM 56 O56 MOL 1 0.238 6.050 3.908
ATOM 57 H57 MOL 1 -0.576 6.377 3.546
ATOM 58 H58 MOL 1 1.585 4.666 3.534
ATOM 59 H59 MOL 1 0.462 4.951 2.165
ATOM 60 H60 MOL 1 -0.069 2.774 3.060
ATOM 61 O61 MOL 1 0.033 3.359 5.056
ATOM 62 C62 MOL 1 -0.636 2.295 5.674
ATOM 63 H63 MOL 1 -0.235 2.314 6.716
ATOM 64 O64 MOL 1 -0.218 1.166 4.938
ATOM 65 C65 MOL 1 0.558 0.201 5.647
ATOM 66 C66 MOL 1 -0.237 -1.138 5.592
ATOM 67 C67 MOL 1 0.666 -2.288 6.105
ATOM 68 O68 MOL 1 0.085 -3.565 5.925
ATOM 69 H69 MOL 1 -0.798 -3.515 6.263
ATOM 70 H70 MOL 1 0.874 -2.154 7.196
ATOM 71 O71 MOL 1 -1.369 -1.120 6.443
ATOM 72 H72 MOL 1 -1.862 -0.322 6.248
ATOM 73 H73 MOL 1 -0.572 -1.345 4.544
ATOM 74 H74 MOL 1 0.715 0.508 6.714
ATOM 75 C75 MOL 1 1.910 0.063 4.898
ATOM 76 C76 MOL 1 2.836 1.293 5.044
ATOM 77 O77 MOL 1 3.114 1.670 6.361
ATOM 78 H78 MOL 1 2.331 2.078 6.712
ATOM 79 H79 MOL 1 2.406 2.139 4.470
ATOM 80 H80 MOL 1 3.839 1.073 4.633
ATOM 81 H81 MOL 1 1.714 -0.078 3.806
ATOM 82 O82 MOL 1 2.669 -1.052 5.377
ATOM 83 C83 MOL 1 2.025 -2.295 5.345
ATOM 84 H84 MOL 1 2.769 -2.978 5.823
ATOM 85 O85 MOL 1 1.845 -2.547 3.967
ATOM 86 C86 MOL 1 2.568 -3.657 3.436
ATOM 87 C87 MOL 1 1.509 -4.656 2.886
ATOM 88 C88 MOL 1 2.225 -5.760 2.069
ATOM 89 O89 MOL 1 1.325 -6.616 1.394
ATOM 90 H90 MOL 1 0.677 -6.890 2.031
ATOM 91 H91 MOL 1 2.856 -6.388 2.746
ATOM 92 O92 MOL 1 0.821 -5.315 3.927
ATOM 93 H93 MOL 1 0.494 -4.642 4.525
ATOM 94 H94 MOL 1 0.766 -4.119 2.244
ATOM 95 H95 MOL 1 3.186 -4.155 4.228
ATOM 96 C96 MOL 1 3.461 -3.122 2.285
ATOM 97 C97 MOL 1 4.645 -2.250 2.762
ATOM 98 O98 MOL 1 5.480 -2.852 3.708
ATOM 99 H99 MOL 1 5.009 -2.868 4.534
ATOM 100 H100MOL 1 5.334 -2.040 1.923
ATOM 101 H101MOL 1 4.252 -1.282 3.137
ATOM 102 H102MOL 1 2.840 -2.494 1.598
ATOM 103 O103MOL 1 4.045 -4.189 1.530
ATOM 104 C104MOL 1 3.152 -5.125 0.991
ATOM 105 H105MOL 1 3.827 -5.882 0.524
ATOM 106 O106MOL 1 2.419 -4.374 0.047
ATOM 107 C107MOL 1 2.557 -4.769 -1.318
ATOM 108 C108MOL 1 1.134 -5.156 -1.819
ATOM 109 C109MOL 1 1.171 -5.360 -3.355
ATOM 110 O110MOL 1 -0.114 -5.536 -3.919
ATOM 111 H111MOL 1 -0.566 -6.174 -3.381
ATOM 112 H112MOL 1 1.781 -6.265 -3.604
ATOM 113 O113MOL 1 0.700 -6.382 -1.272
ATOM 114 H114MOL 1 0.824 -6.334 -0.323
ATOM 115 H115MOL 1 0.398 -4.358 -1.551
ATOM 116 H116MOL 1 3.250 -5.643 -1.421
ATOM 117 C117MOL 1 3.083 -3.540 -2.106
ATOM 118 C118MOL 1 4.542 -3.152 -1.772
ATOM 119 O119MOL 1 5.471 -4.189 -1.890
ATOM 120 H120MOL 1 5.348 -4.767 -1.146
ATOM 121 H121MOL 1 4.917 -2.401 -2.492
ATOM 122 H122MOL 1 4.573 -2.703 -0.758
ATOM 123 H123MOL 1 2.440 -2.654 -1.877
ATOM 124 O124MOL 1 3.058 -3.778 -3.516
ATOM 125 C125MOL 1 1.818 -4.133 -4.062
ATOM 126 H126MOL 1 2.066 -4.351 -5.130
ATOM 127 O127MOL 1 1.035 -2.965 -3.913
ATOM 128 C128MOL 1 0.634 -2.336 -5.131
ATOM 129 H129MOL 1 1.030 -2.903 -6.020
ATOM 130 C130MOL 1 -0.921 -2.336 -5.131
ATOM 131 O131MOL 1 -1.436 -3.622 -5.404
ATOM 132 H132MOL 1 -1.037 -4.226 -4.776
ATOM 133 H133MOL 1 -1.307 -1.990 -4.139
ATOM 134 C134MOL 1 -1.441 -1.410 -6.258
ATOM 135 O135MOL 1 -2.842 -1.225 -6.217
ATOM 136 H136MOL 1 -3.232 -2.085 -6.123
ATOM 137 H137MOL 1 -1.180 -1.837 -7.258
ATOM 138 C138MOL 1 -0.787 -0.002 -6.144
ATOM 139 H139MOL 1 -1.003 0.635 -7.036
ATOM 140 O140MOL 1 0.612 -0.061 -6.129
ATOM 141 C141MOL 1 1.210 -0.894 -5.131
ATOM 142 H142MOL 1 1.050 -0.420 -4.131
ATOM 143 C143MOL 1 2.725 -0.877 -5.443
ATOM 144 H144MOL 1 3.101 0.156 -5.554
ATOM 145 H145MOL 1 3.274 -1.355 -4.606
ATOM 146 O146MOL 1 3.081 -1.477 -6.656
ATOM 147 H147MOL 1 2.665 -2.334 -6.676
CONECT 1 2 3
CONECT 2 1
CONECT 3 1 4 5 6
CONECT 4 3
CONECT 5 3
CONECT 6 3 7 8 9
CONECT 7 6 20
CONECT 8 6
CONECT 9 6 10 11 12
CONECT 10 9 138
CONECT 11 9
CONECT 12 9 13 15 16
CONECT 13 12 14
CONECT 14 13
CONECT 15 12
CONECT 16 12 17 19 20
CONECT 17 16 18
CONECT 18 17
CONECT 19 16
CONECT 20 7 16 21 22
CONECT 21 20
CONECT 22 20 23
CONECT 23 22 24 32 33
CONECT 24 23 25 26 31
CONECT 25 24 41
CONECT 26 24 27 29 30
CONECT 27 26 28
CONECT 28 27
CONECT 29 26
CONECT 30 26
CONECT 31 24
CONECT 32 23
CONECT 33 23 34 36 37
CONECT 34 33 35
CONECT 35 34
CONECT 36 33
CONECT 37 33 38 40 41
CONECT 38 37 39
CONECT 39 38
CONECT 40 37
CONECT 41 25 37 42 43
CONECT 42 41
CONECT 43 41 44
CONECT 44 43 45 53 54
CONECT 45 44 46 50 52
CONECT 46 45 47 49 62
CONECT 47 46 48
CONECT 48 47
CONECT 49 46
CONECT 50 45 51
CONECT 51 50
CONECT 52 45
CONECT 53 44
CONECT 54 44 55 60 61
CONECT 55 54 56 58 59
CONECT 56 55 57
CONECT 57 56
CONECT 58 55
CONECT 59 55
CONECT 60 54
CONECT 61 54 62
CONECT 62 46 61 63 64
CONECT 63 62
CONECT 64 62 65
CONECT 65 64 66 74 75
CONECT 66 65 67 71 73
CONECT 67 66 68 70 83
CONECT 68 67 69
CONECT 69 68
CONECT 70 67
CONECT 71 66 72
CONECT 72 71
CONECT 73 66
CONECT 74 65
CONECT 75 65 76 81 82
CONECT 76 75 77 79 80
CONECT 77 76 78
CONECT 78 77
CONECT 79 76
CONECT 80 76
CONECT 81 75
CONECT 82 75 83
CONECT 83 67 82 84 85
CONECT 84 83
CONECT 85 83 86
CONECT 86 85 87 95 96
CONECT 87 86 88 92 94
CONECT 88 87 89 91 104
CONECT 89 88 90
CONECT 90 89
CONECT 91 88
CONECT 92 87 93
CONECT 93 92
CONECT 94 87
CONECT 95 86
CONECT 96 86 97 102 103
CONECT 97 96 98 100 101
CONECT 98 97 99
CONECT 99 98
CONECT 100 97
CONECT 101 97
CONECT 102 96
CONECT 103 96 104
CONECT 104 88 103 105 106
CONECT 105 104
CONECT 106 104 107
CONECT 107 106 108 116 117
CONECT 108 107 109 113 115
CONECT 109 108 110 112 125
CONECT 110 109 111
CONECT 111 110
CONECT 112 109
CONECT 113 108 114
CONECT 114 113
CONECT 115 108
CONECT 116 107
CONECT 117 107 118 123 124
CONECT 118 117 119 121 122
CONECT 119 118 120
CONECT 120 119
CONECT 121 118
CONECT 122 118
CONECT 123 117
CONECT 124 117 125
CONECT 125 109 124 126 127
CONECT 126 125
CONECT 127 125 128
CONECT 128 127 129 130 141
CONECT 129 128
CONECT 130 128 131 133 134
CONECT 131 130 132
CONECT 132 131
CONECT 133 130
CONECT 134 130 135 137 138
CONECT 135 134 136
CONECT 136 135
CONECT 137 134
CONECT 138 10 134 139 140
CONECT 139 138
CONECT 140 138 141
CONECT 141 128 140 142 143
CONECT 142 141
CONECT 143 141 144 145 146
CONECT 144 143
CONECT 145 143
CONECT 146 143 147
CONECT 147 146
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