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
> >
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>
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