Hi,
"Du" stands for Dummy atom. It has of course no associated atomic number.
Either edit the molecules containing Du atoms by deleting them or changing
Du to a valid atom type, or do not convert these molecules at all.
I guess that, perhaps, obabel could just skip the molecules containing Du
atoms in a future version?
I think that Du atom can occur only in mol2 format.
Regards,
Pascal
2016-07-21 15:12 GMT+02:00 jrhaulung <jrhaul...@gmail.com>:
> Dear all:
> When using the babel to covert a mol2 dataset to pdbqt dataset, the
> program was crashed in the middle when encountering a compound for some
> reason (showed in below). The error message shows that "**** Open Babel
> Warning in OpenBabel ::OBElementTable::GetAtomicNum Cannot understand the
> element label Du." Can anyone could give me a help....Thanks a lot.
>
> sincerely,
> Jrhau
>
> @<TRIPOS>MOLECULE
> 105
> 167 178 0 0 0
> SMALL
> GASTEIGER
> ****
>
> @<TRIPOS>ATOM
> 1 C 3.3930 1.2210 -1.1580 C.3 1 LIG1
> 0.0865
> 2 C 3.9900 -0.1800 -0.8070 C.3 1 LIG1
> 0.0956
> 3 C 2.9670 -1.2870 -0.3910 C.3 1 LIG1
> 0.0231
> 4 C 1.6720 -1.2730 -1.2660 C.3 1 LIG1
> -0.0245
> 5 C 1.0780 0.1540 -1.5900 C.3 1 LIG1
> -0.0129
> 6 C 1.8590 1.3480 -0.8770 C.3 1 LIG1
> 0.0079
> 7 C 0.6620 -2.3480 -0.7730 C.3 1 LIG1
> -0.0485
> 8 C -0.6760 -1.8090 -0.2360 C.3 1 LIG1
> -0.0462
> 9 C -1.3970 -0.8950 -1.2620 C.3 1 LIG1
> -0.0188
> 10 C -0.5140 0.3130 -1.7030 C.3 1 LIG1
> -0.0248
> 11 C -2.8670 -0.3810 -0.8650 C.3 1 LIG1
> 0.0020
> 12 C -3.3790 0.4020 -2.1000 C.2 1 LIG1
> -0.0625
> 13 C -2.5630 0.9080 -3.0530 C.2 1 LIG1
> -0.0836
> 14 C -1.0640 0.8240 -3.0430 C.3 1 LIG1
> -0.0306
> 15 C -3.8200 -1.6210 -0.6170 C.3 1 LIG1
> -0.0206
> 16 C -5.3010 -1.5720 -1.1000 C.3 1 LIG1
> -0.0102
> 17 C -5.8710 -0.1620 -1.4530 C.3 1 LIG1
> 0.0212
> 18 C -4.8580 0.6760 -2.3010 C.3 1 LIG1
> -0.0077
> 19 C -6.4060 0.5490 -0.1500 C.3 1 LIG1
> -0.0408
> 20 C -6.3260 2.0800 -0.1290 C.3 1 LIG1
> -0.0447
> 21 C -6.3400 2.7170 -1.5190 C.3 1 LIG1
> -0.0083
> 22 C -5.1110 2.2090 -2.2910 C.3 1 LIG1
> -0.0381
> 23 C -6.2360 4.2290 -1.3630 C.3 1 LIG1
> -0.0575
> 24 C -7.6410 2.4220 -2.2640 C.3 1 LIG1
> 0.0496
> 25 O -8.5120 3.5160 -2.0780 O.3 1 LIG1
> -0.3945
> 26 C -7.1110 -0.3360 -2.3030 C.2 1 LIG1
> 0.0488
> 27 O -7.0880 -0.1130 -3.4920 O.co2 1 LIG1
> -0.5492
> 28 O -8.1230 -0.7110 -1.7110 O.co2 1 LIG1
> -0.5492
> 29 C -1.5140 -1.8160 -2.5000 C.3 1 LIG1
> -0.0585
> 30 C 1.5530 0.3280 -3.0530 C.3 1 LIG1
> -0.0345
> 31 C 3.6600 -2.6470 -0.5550 C.3 1 LIG1
> -0.0547
> 32 C 2.5660 -1.2270 1.0860 C.3 1 LIG1
> 0.0523
> 33 O 4.1070 2.3130 -0.6020 O.3 1 LIG1
> -0.3889
> 34 C -2.9840 0.6540 0.3150 C.3 1 LIG1
> -0.0320
> 35 O 3.7400 -1.0940 1.8560 O.3 1 LIG1
> -0.3944
> 36 O 5.0270 -0.1230 0.1620 O.3 1 LIG1
> -0.3423
> 37 C 8.6880 -0.2680 -1.8530 C.3 1 LIG1
> 0.1069
> 38 C 8.7910 -0.0450 -0.3280 C.3 1 LIG1
> 0.1137
> 39 C 7.4550 0.4470 -2.4390 C.3 1 LIG1
> 0.0792
> 40 O 6.2850 0.0200 -1.7580 O.3 1 LIG1
> -0.3461
> 41 C 6.2620 0.3160 -0.3670 C.3 1 LIG1
> 0.1879
> 42 C 7.4430 -0.3950 0.3440 C.3 1 LIG1
> 0.1341
> 43 O 7.4790 0.0000 1.7050 O.3 1 LIG1
> -0.3841
> 44 O 9.8400 0.2340 -2.5020 O.3 1 LIG1
> -0.3869
> 45 O 9.8220 -0.8610 0.2050 O.3 1 LIG1
> -0.3864
> 46 H 3.5700 1.3690 -2.2270 H 1 LIG1
> 0.0623
> 47 H 4.5000 -0.5270 -1.7070 H 1 LIG1
> 0.0629
> 48 H 2.0140 -1.7320 -2.1990 H 1 LIG1
> 0.0313
> 49 H 1.5450 2.2250 -1.4370 H 1 LIG1
> 0.0344
> 50 H 1.1040 -2.9860 -0.0080 H 1 LIG1
> 0.0268
> 51 H 0.4530 -3.0450 -1.5900 H 1 LIG1
> 0.0268
> 52 H -0.4880 -1.3750 0.7340 H 1 LIG1
> 0.0271
> 53 H -1.2830 -2.6910 -0.0370 H 1 LIG1
> 0.0271
> 54 H -0.7660 1.1700 -1.1050 H 1 LIG1
> 0.0315
> 55 H -3.0020 1.4260 -3.8890 H 1 LIG1
> 0.0572
> 56 H -0.6480 1.7970 -3.2640 H 1 LIG1
> 0.0310
> 57 H -0.7680 0.1780 -3.8630 H 1 LIG1
> 0.0310
> 58 H -3.3650 -2.4040 -1.2150 H 1 LIG1
> 0.0316
> 59 H -5.9710 -1.8850 -0.2890 H 1 LIG1
> 0.0328
> 60 H -5.0430 0.3650 -3.3340 H 1 LIG1
> 0.0355
> 61 H -7.4590 0.2850 0.0040 H 1 LIG1
> 0.0275
> 62 H -5.9610 0.1520 0.7640 H 1 LIG1
> 0.0275
> 63 H -5.4180 2.3830 0.3890 H 1 LIG1
> 0.0272
> 64 H -7.1470 2.4810 0.4690 H 1 LIG1
> 0.0272
> 65 H -4.2420 2.7070 -1.8610 H 1 LIG1
> 0.0277
> 66 H -5.1520 2.5840 -3.3180 H 1 LIG1
> 0.0277
> 67 H -7.0900 4.6170 -0.8090 H 1 LIG1
> 0.0236
> 68 H -5.3180 4.5000 -0.8440 H 1 LIG1
> 0.0236
> 69 H -6.2250 4.7150 -2.3380 H 1 LIG1
> 0.0236
> 70 H -8.1230 1.5330 -1.8590 H 1 LIG1
> 0.0562
> 71 H -7.4570 2.3130 -3.3320 H 1 LIG1
> 0.0562
> 72 H -9.3360 3.3070 -2.5470 H 1 LIG1
> 0.2094
> 73 H -2.4060 -2.4390 -2.4590 H 1 LIG1
> 0.0235
> 74 H -0.6500 -2.4770 -2.5700 H 1 LIG1
> 0.0235
> 75 H -1.5610 -1.2270 -3.4160 H 1 LIG1
> 0.0235
> 76 H 1.3590 1.3420 -3.3730 H 1 LIG1
> 0.0306
> 77 H 4.5470 -2.7270 0.0720 H 1 LIG1
> 0.0237
> 78 H 3.9670 -2.7990 -1.5900 H 1 LIG1
> 0.0237
> 79 H 2.9840 -3.4570 -0.2830 H 1 LIG1
> 0.0237
> 80 H 2.0660 -2.1470 1.3870 H 1 LIG1
> 0.0563
> 81 H 1.9340 -0.3610 1.2790 H 1 LIG1
> 0.0563
> 82 H 3.8560 3.1060 -1.1030 H 1 LIG1
> 0.2099
> 83 H -4.0140 0.6910 0.6290 H 1 LIG1
> 0.0283
> 84 H -2.8180 1.6600 -0.0700 H 1 LIG1
> 0.0283
> 85 H 3.4730 -1.0940 2.7870 H 1 LIG1
> 0.2094
> 86 H 8.6250 -1.3340 -2.0780 H 1 LIG1
> 0.0643
> 87 H 9.0510 0.9960 -0.1230 H 1 LIG1
> 0.0647
> 88 H 7.5310 1.5330 -2.3480 H 1 LIG1
> 0.0587
> 89 H 7.3280 0.2110 -3.4960 H 1 LIG1
> 0.0587
> 90 H 6.3150 1.4000 -0.2460 H 1 LIG1
> 0.0937
> 91 H 7.2870 -1.4770 0.3200 H 1 LIG1
> 0.0671
> 92 H 6.6450 -0.2870 2.1080 H 1 LIG1
> 0.2101
> 93 H 9.7350 0.0590 -3.4510 H 1 LIG1
> 0.2100
> 94 H 10.6450 -0.6130 -0.2440 H 1 LIG1
> 0.2100
> 95 C 1.5920 1.7500 0.6290 C.3 1 LIG1
> 0.0317
> 96 O 3.8770 4.5630 2.7620 O.2 1 LIG1
> -0.2754
> 97 C 3.4060 3.4530 2.6620 C.2 1 LIG1
> 0.2189
> 98 H 1.9920 3.4490 4.2540 H 1 LIG1
> 0.1490
> 99 N 2.4080 2.9450 3.4980 N.am 1 LIG1
> -0.3111
> 100 C 2.6110 1.3810 1.6930 C.3 1 LIG1
> 0.0053
> 101 C 2.0660 1.5820 3.1190 C.3 1 LIG1
> 0.0385
> 102 C 3.7680 2.3980 1.6500 C.3 1 LIG1
> 0.0642
> 103 H 2.9470 0.3690 1.5270 H 1 LIG1
> 0.0339
> 104 H 2.5960 0.9220 3.7910 H 1 LIG1
> 0.0509
> 105 H 3.8670 2.8480 0.6740 H 1 LIG1
> 0.0420
> 106 H 1.5820 2.8400 0.6470 H 1 LIG1
> 0.0440
> 107 C 0.5720 1.2950 3.2460 C.3 1 LIG1
> 0.0475
> 108 N -0.1350 -0.9880 4.0390 N.ar 1 LIG1
> -0.2405
> 109 H -0.0210 -2.9570 1.5180 H 1 LIG1
> 0.1662
> 110 N 0.0120 -2.1930 2.1500 N.ar 1 LIG1
> -0.3506
> 111 C -0.2930 -2.2190 3.4790 C.ar 1 LIG1
> 0.0936
> 112 C 0.3690 -0.9220 1.8710 C.ar 1 LIG1
> 0.0247
> 113 C 0.2770 -0.1760 3.0430 C.ar 1 LIG1
> 0.0661
> 114 H -0.6170 -3.1000 4.0160 H 1 LIG1
> 0.1027
> 115 H 0.6700 -0.5800 0.8890 H 1 LIG1
> 0.0825
> 116 H 0.0160 1.7770 2.4420 H 1 LIG1
> 0.0408
> 117 C 0.0740 1.7750 4.6100 C.3 1 LIG1
> 0.0688
> 118 H -1.0410 0.8440 8.2660 H 1 LIG1
> 0.1206
> 119 N -0.7890 0.6540 7.2850 N.3 1 LIG1
> -0.3059
> 120 H -0.9590 -0.3440 7.0960 H 1 LIG1
> 0.1206
> 121 C -1.3090 1.2290 4.9590 C.3 1 LIG1
> 0.0133
> 122 C -1.6700 1.4340 6.4320 C.3 1 LIG1
> 0.1061
> 123 H 0.0700 2.8650 4.6150 H 1 LIG1
> 0.0602
> 124 H -1.3890 0.1760 4.6880 H 1 LIG1
> 0.0328
> 125 H -2.0700 1.6620 4.3130 H 1 LIG1
> 0.0328
> 126 H -2.7050 1.1470 6.6170 H 1 LIG1
> 0.0763
> 127 C 5.0820 1.7170 2.0180 C.3 1 LIG1
> 0.0556
> 128 H 6.5610 2.0610 3.2130 H 1 LIG1
> 0.2094
> 129 O 5.7560 2.5330 2.9490 O.3 1 LIG1
> -0.3942
> 130 H 5.7190 1.6090 1.1390 H 1 LIG1
> 0.0565
> 131 H 4.8990 0.7500 2.4840 H 1 LIG1
> 0.0565
> 132 O -1.4920 2.7970 6.7420 O.3 1 LIG1
> -0.3775
> 133 H -1.6640 2.8980 7.6920 H 1 LIG1
> 0.2114
> 134 C -3.8400 -2.2580 0.7810 C.3 1 LIG1
> -0.0052
> 135 N -5.1020 -5.7720 0.1090 N.ar 1 LIG1
> -0.2212
> 136 H -3.9100 -4.3010 2.7290 H 1 LIG1
> 0.1665
> 137 N -4.2400 -4.5390 1.8150 N.ar 1 LIG1
> -0.3466
> 138 C -4.6800 -5.7790 1.4100 C.ar 1 LIG1
> 0.0957
> 139 C -4.3400 -3.7190 0.7360 C.ar 1 LIG1
> 0.0575
> 140 C -4.9240 -4.4900 -0.2750 C.ar 1 LIG1
> 0.1398
> 141 H -4.6900 -6.6580 2.0490 H 1 LIG1
> 0.1027
> 142 H -2.8540 -2.2810 1.2320 H 1 LIG1
> 0.0332
> 143 H -4.4730 -1.6880 1.4590 H 1 LIG1
> 0.0332
> 144 C -5.5040 -2.6820 -2.1660 C.3 1 LIG1
> 0.0145
> 145 N -5.3440 -4.0720 -1.6430 N.pl3 1 LIG1
> -0.3274
> 146 H -5.5980 -4.7950 -2.2870 H 1 LIG1
> 0.1475
> 147 H -6.5020 -2.6450 -2.6000 H 1 LIG1
> 0.0465
> 148 H -4.8130 -2.5350 -2.9960 H 1 LIG1
> 0.0465
> 149 O 0.9840 1.3340 5.5920 O.3 1 LIG1
> -0.3909
> 150 H 1.8540 1.6970 5.3600 H 1 LIG1
> 0.2098
> 151 C 3.0470 0.0160 -3.1740 C.3 1 LIG1
> -0.0497
> 152 C 0.8480 -0.6820 -3.9710 C.3 1 LIG1
> -0.0497
> 153 C 3.0840 -1.4200 -3.6740 C.3 1 LIG1
> -0.0528
> 154 C 1.9710 -1.4020 -4.7110 C.3 1 LIG1
> -0.0528
> 155 H 4.0410 -1.6860 -4.1020 H 1 LIG1
> 0.0265
> 156 H 2.8610 -2.1150 -2.8750 H 1 LIG1
> 0.0265
> 157 H 3.5040 0.6700 -3.9040 H 1 LIG1
> 0.0268
> 158 H 3.5860 0.1430 -2.2460 H 1 LIG1
> 0.0268
> 159 H 0.2730 -1.3980 -3.3980 H 1 LIG1
> 0.0268
> 160 H 0.1680 -0.1990 -4.6560 H 1 LIG1
> 0.0268
> 161 H 2.2720 -0.8460 -5.5880 H 1 LIG1
> 0.0265
> 162 H 1.6820 -2.3950 -5.0250 H 1 LIG1
> 0.0265
> 163 C -2.1640 0.5270 1.6230 C.3 1 LIG1
> 0.0100
> 164 C 0.2710 1.3380 1.0680 C.1 1 LIG1
> -0.0981
> 165 C -0.8140 0.9790 1.3560 C.1 1 LIG1
> -0.1019
> 166 H -2.5980 1.1600 2.3950 H 1 LIG1
> 0.0398
> 167 H -2.1500 -0.4880 2.0180 H 1 LIG1
> 0.0398
> @<TRIPOS>BOND
> 1 1 2 1
> 2 1 6 1
> 3 1 33 1
> 4 1 46 1
> 5 2 3 1
> 6 2 36 1
> 7 2 47 1
> 8 3 4 1
> 9 3 31 1
> 10 3 32 1
> 11 4 5 1
> 12 4 7 1
> 13 4 48 1
> 14 5 6 1
> 15 5 10 1
> 16 5 30 1
> 17 6 49 1
> 18 6 95 1
> 19 7 8 1
> 20 7 50 1
> 21 7 51 1
> 22 8 9 1
> 23 8 52 1
> 24 8 53 1
> 25 9 10 1
> 26 9 11 1
> 27 9 29 1
> 28 10 14 1
> 29 10 54 1
> 30 11 12 1
> 31 11 15 1
> 32 11 34 1
> 33 12 13 2
> 34 12 18 1
> 35 13 14 1
> 36 13 55 1
> 37 14 56 1
> 38 14 57 1
> 39 15 16 1
> 40 15 58 1
> 41 15 134 1
> 42 16 17 1
> 43 16 59 1
> 44 16 144 1
> 45 17 18 1
> 46 17 19 1
> 47 17 26 1
> 48 18 22 1
> 49 18 60 1
> 50 19 20 1
> 51 19 61 1
> 52 19 62 1
> 53 20 21 1
> 54 20 63 1
> 55 20 64 1
> 56 21 22 1
> 57 21 23 1
> 58 21 24 1
> 59 22 65 1
> 60 22 66 1
> 61 23 67 1
> 62 23 68 1
> 63 23 69 1
> 64 24 25 1
> 65 24 70 1
> 66 24 71 1
> 67 25 72 1
> 68 26 27 ar
> 69 26 28 ar
> 70 29 73 1
> 71 29 74 1
> 72 29 75 1
> 73 30 76 1
> 74 30 151 1
> 75 30 152 1
> 76 31 77 1
> 77 31 78 1
> 78 31 79 1
> 79 32 35 1
> 80 32 80 1
> 81 32 81 1
> 82 33 82 1
> 83 34 83 1
> 84 34 84 1
> 85 34 163 1
> 86 35 85 1
> 87 36 41 1
> 88 37 38 1
> 89 37 39 1
> 90 37 44 1
> 91 37 86 1
> 92 38 42 1
> 93 38 45 1
> 94 38 87 1
> 95 39 40 1
> 96 39 88 1
> 97 39 89 1
> 98 40 41 1
> 99 41 42 1
> 100 41 90 1
> 101 42 43 1
> 102 42 91 1
> 103 43 92 1
> 104 44 93 1
> 105 45 94 1
> 106 95 100 1
> 107 95 106 1
> 108 95 164 1
> 109 96 97 2
> 110 97 99 am
> 111 97 102 1
> 112 98 99 1
> 113 99 101 1
> 114 100 101 1
> 115 100 102 1
> 116 100 103 1
> 117 101 104 1
> 118 101 107 1
> 119 102 105 1
> 120 102 127 1
> 121 107 113 1
> 122 107 116 1
> 123 107 117 1
> 124 108 111 ar
> 125 108 113 ar
> 126 109 110 1
> 127 110 111 ar
> 128 110 112 ar
> 129 111 114 1
> 130 112 113 ar
> 131 112 115 1
> 132 117 121 1
> 133 117 123 1
> 134 117 149 1
> 135 118 119 1
> 136 119 120 1
> 137 119 122 1
> 138 121 122 1
> 139 121 124 1
> 140 121 125 1
> 141 122 126 1
> 142 122 132 1
> 143 127 129 1
> 144 127 130 1
> 145 127 131 1
> 146 128 129 1
> 147 132 133 1
> 148 134 139 1
> 149 134 142 1
> 150 134 143 1
> 151 135 138 ar
> 152 135 140 ar
> 153 136 137 1
> 154 137 138 ar
> 155 137 139 ar
> 156 138 141 1
> 157 139 140 ar
> 158 140 145 1
> 159 144 145 1
> 160 144 147 1
> 161 144 148 1
> 162 145 146 1
> 163 149 150 1
> 164 151 153 1
> 165 151 157 1
> 166 151 158 1
> 167 152 154 1
> 168 152 159 1
> 169 152 160 1
> 170 153 154 1
> 171 153 155 1
> 172 153 156 1
> 173 154 161 1
> 174 154 162 1
> 175 163 165 1
> 176 163 166 1
> 177 163 167 1
> 178 164 165 3
>
>
>
>
> --
> View this message in context:
> http://forums.openbabel.org/Cannot-understand-the-element-label-Du-tp4659404.html
> Sent from the General discussion mailing list archive at Nabble.com.
>
>
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patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
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