questions on this (like all questions) should go to mailing list; I have never
looked at how gen3D is implemented or the minimizer that presumably is giving
this error, so I am of no help.
-David
> On Apr 2, 2015, at 10:25 PM, Matthew Guberman wrote:
>
>Thanks David for your help. I, how
You didn’t tell open babel to generate coordinates. It appears to did tell it
to add hydrogens
Telling it to generate 3D coordinates:
$ obabel -:'[S@]1(C)[Au][S@]([Au][S@](C)[Au][S@]([Au]1)C)C' -oxyz -h --gen3D
24
S -2.62740 -0.178950.14170
C -2.95652 -0.069
Hello,
I need to convert a SMILES string (below) to xyz coordinates. When
I try to do this, the correct structure is shown in Firefox, but the
list of coordinates (below) contains only zeros, and when I save the
output as a PDB (so I can view it in Chimera), I only see a single Au
atom. H
