I'm on trunk version and conversion is successful.
[maciek@fokus ~]$ obabel
-:"OP(=O)(O)OC[C@H]1O[C@H]([C@@H]([C@@H]1O)OCC(=O)c1c2cc3ccccc3cc2ccc1)n1cnc2c(=O)[nH]c(N)nc12"
-ismi -omol2 --gen3d
@<TRIPOS>MOLECULE
*****
65 70 0 0 0
SMALL
GASTEIGER
@<TRIPOS>ATOM
1 O 2.4378 -1.0815 -1.3719 O.3 1 LIG1 -0.3026
2 P 3.0749 -0.3174 -2.6155 P.3 1 LIG1 0.4724
3 O 2.7869 -0.9641 -3.9250 O.2 1 LIG1 -0.2275
4 O 2.3947 1.1237 -2.5121 O.3 1 LIG1 -0.3026
5 O 4.6155 -0.0562 -2.2781 O.3 1 LIG1 -0.2841
6 C 4.9281 0.6358 -1.0775 C.3 1 LIG1 0.0878
7 C 6.4400 0.7658 -0.9139 C.3 1 LIG1 0.1134
8 H 6.6337 1.2787 0.0371 H 1 LIG1 0.0647
9 O 7.0680 -0.5260 -0.8323 O.3 1 LIG1 -0.3456
10 C 8.4243 -0.3312 -1.2825 C.3 1 LIG1 0.1669
11 H 9.0126 0.0714 -0.4460 H 1 LIG1 0.0866
12 C 8.3286 0.6891 -2.4259 C.3 1 LIG1 0.1325
13 H 8.0933 0.1773 -3.3661 H 1 LIG1 0.0668
14 C 7.1053 1.5310 -2.0602 C.3 1 LIG1 0.1138
15 H 6.4564 1.6286 -2.9389 H 1 LIG1 0.0647
16 O 7.4432 2.8443 -1.6133 O.3 1 LIG1 -0.3864
17 O 9.5386 1.4395 -2.5310 O.3 1 LIG1 -0.3616
18 C 9.6744 2.1744 -3.7350 C.3 1 LIG1 0.1110
19 C 11.0051 2.9408 -3.8305 C.2 1 LIG1 0.1891
20 O 11.0666 3.9722 -4.5000 O.2 1 LIG1 -0.2896
21 C 12.2272 2.3768 -3.1511 C.ar 1 LIG1 0.0274
22 C 13.2846 3.1806 -2.6386 C.ar 1 LIG1 -0.0067
23 C 13.3843 4.5856 -2.7792 C.ar 1 LIG1 -0.0456
24 C 14.4974 5.3100 -2.3189 C.ar 1 LIG1 -0.0173
25 C 14.6069 6.6928 -2.5271 C.ar 1 LIG1 -0.0540
26 C 15.7312 7.3914 -2.0859 C.ar 1 LIG1 -0.0612
27 C 16.7562 6.7180 -1.4275 C.ar 1 LIG1 -0.0612
28 C 16.6588 5.3451 -1.2088 C.ar 1 LIG1 -0.0540
29 C 15.5358 4.6327 -1.6521 C.ar 1 LIG1 -0.0173
30 C 15.4345 3.2538 -1.4549 C.ar 1 LIG1 -0.0463
31 C 14.3416 2.5283 -1.9439 C.ar 1 LIG1 -0.0166
32 C 14.3239 1.1430 -1.7498 C.ar 1 LIG1 -0.0540
33 C 13.3202 0.3686 -2.3061 C.ar 1 LIG1 -0.0605
34 C 12.3132 0.9818 -3.0393 C.ar 1 LIG1 -0.0506
35 N 9.0010 -1.6299 -1.5935 N.ar 1 LIG1 -0.2854
36 C 9.1117 -2.6662 -0.6901 C.ar 1 LIG1 0.1005
37 N 9.7437 -3.7105 -1.1934 N.ar 1 LIG1 -0.2286
38 C 10.0575 -3.3272 -2.4693 C.ar 1 LIG1 0.1721
39 C 10.8003 -4.0264 -3.5002 C.ar 1 LIG1 0.2803
40 O 11.3004 -5.1305 -3.4030 O.2 1 LIG1 -0.2654
41 N 10.9390 -3.2641 -4.6565 N.ar 1 LIG1 -0.2934
42 H 11.5202 -3.6693 -5.3707 H 1 LIG1 0.1716
43 C 10.5123 -1.9716 -4.7838 C.ar 1 LIG1 0.1950
44 N 10.8575 -1.3503 -5.9379 N.pl3 1 LIG1 -0.3289
45 N 9.8361 -1.3330 -3.8695 N.ar 1 LIG1 -0.1963
46 C 9.6292 -2.0498 -2.7375 C.ar 1 LIG1 0.1712
47 H 1.5706 -1.4615 -1.6035 H 1 LIG1 0.2220
48 H 2.2503 1.4923 -3.4028 H 1 LIG1 0.2220
49 H 4.5059 0.0926 -0.2269 H 1 LIG1 0.0592
50 H 4.4823 1.6356 -1.1203 H 1 LIG1 0.0592
51 H 6.9883 3.4857 -2.1865 H 1 LIG1 0.2100
52 H 8.8700 2.9152 -3.7947 H 1 LIG1 0.0643
53 H 9.5996 1.5131 -4.6068 H 1 LIG1 0.0643
54 H 12.6014 5.1378 -3.2940 H 1 LIG1 0.0630
55 H 13.8182 7.2328 -3.0467 H 1 LIG1 0.0624
56 H 15.8062 8.4609 -2.2602 H 1 LIG1 0.0618
57 H 17.6336 7.2590 -1.0851 H 1 LIG1 0.0618
58 H 17.4696 4.8314 -0.6973 H 1 LIG1 0.0624
59 H 16.2387 2.7318 -0.9381 H 1 LIG1 0.0630
60 H 15.1147 0.6480 -1.1888 H 1 LIG1 0.0624
61 H 13.3210 -0.7101 -2.1754 H 1 LIG1 0.0618
62 H 11.5816 0.3470 -3.5196 H 1 LIG1 0.0625
63 H 8.7236 -2.6007 0.3194 H 1 LIG1 0.1030
64 H 10.6816 -1.8859 -6.7791 H 1 LIG1 0.1451
65 H 10.4817 -0.4112 -6.0074 H 1 LIG1 0.1451
@<TRIPOS>BOND
1 1 2 1
2 2 3 2
3 2 4 1
4 2 5 1
5 5 6 1
6 6 7 1
7 7 8 1
8 7 9 1
9 9 10 1
10 10 12 1
11 12 13 1
12 12 14 1
13 14 15 1
14 7 14 1
15 14 16 1
16 12 17 1
17 17 18 1
18 18 19 1
19 19 20 2
20 19 21 1
21 21 22 ar
22 22 23 ar
23 23 24 ar
24 24 25 ar
25 25 26 ar
26 26 27 ar
27 27 28 ar
28 28 29 ar
29 24 29 ar
30 29 30 ar
31 30 31 ar
32 22 31 ar
33 31 32 ar
34 32 33 ar
35 33 34 ar
36 21 34 ar
37 35 36 ar
38 36 37 ar
39 37 38 ar
40 38 39 ar
41 39 40 2
42 39 41 ar
43 41 42 1
44 41 43 ar
45 43 44 1
46 43 45 ar
47 45 46 ar
48 35 46 ar
49 38 46 ar
50 10 35 1
51 10 11 1
52 1 47 1
53 4 48 1
54 6 49 1
55 6 50 1
56 16 51 1
57 18 52 1
58 18 53 1
59 23 54 1
60 25 55 1
61 26 56 1
62 27 57 1
63 28 58 1
64 30 59 1
65 32 60 1
66 33 61 1
67 34 62 1
68 36 63 1
69 44 64 1
70 44 65 1
1 molecule converted
----
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2013/1/20 David García Aristegui <ariste...@cbm.uam.es>
> OK, in the News section of the Openbabel main page is announced
> "2011-10-17 Open Babel 2.3.1 Released only", i'm downloading the 2.3.2
> release.
>
> I will try to do the conversion with the new release, but the bug is
> "Milestone: 2.3.x".
>
> By the way, would you be so kind to try to do the conversion, if you have
> a 2.3.2 version available?
>
> Best regards.
>
> > Have you tried it with OB 2.3.2?
> >
> > ----
> > Pozdrawiam, | Best regards,
> > Maciek Wójcikowski
> > mac...@wojcikowski.pl
> >
> >
> > 2013/1/20 David García Aristegui <ariste...@cbm.uam.es>
> >
> >> OK, is an open bug http://sourceforge.net/p/openbabel/bugs/833/
> >>
> >> > Hello, i'm trying to assign 3D coordinates to this SMILES structure
> >> >
> >> > OP(=O)(O)OC[C@H]1O[C@H]([C@@H]([C@
> >> @H]1O)OCC(=O)c1c2cc3ccccc3cc2ccc1)n1cnc2c(=O)[nH]c(N)nc12
> >> >
> >> > obabel is unable to resolve the structure
> >> >
> >> > time obabel --gen3D -ismi 3.3_30.smi -omol2 -O 3.3_30.mol2
> >> > 1 molecule converted
> >> >
> >> > real 6m8.107s
> >> > user 6m7.947s
> >> > sys 0m0.020s
> >> >
> >> > But the mol2 files looks like...
> >> >
> >> > @<TRIPOS>MOLECULE
> >> > *****
> >> > 65 70 0 0 0
> >> > SMALL
> >> > GASTEIGER
> >> >
> >> > @<TRIPOS>ATOM
> >> > 1 O -nan -nan -nan O.3 1 LIG1
> >> > -0.3026
> >> > 2 P -nan -nan -nan P.3 1 LIG1
> >> > 0.4724
> >> > 3 O -nan -nan -nan O.2 1 LIG1
> >> > -0.2275
> >> > (...)
> >> >
> >> > Any ideas, is this a known bug?
> >> > Best
> >> >
> >>
> regards.------------------------------------------------------------------------------
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> >> > OpenBabel-discuss@lists.sourceforge.net
> >> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
> >> >
> >>
> >>
> >>
> >>
> >>
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>
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