Hi,
It looks like it can't find the template ring templates. You can set the
BABEL_DATADIR environment variable to fix this. This should result in
better coordinates.
Tim
On Feb 26, 2016 14:22, "Moshe Ben-zion" <moshe.ben-z...@biu.ac.il> wrote:
> I would greatly appreciate some help with my problem.
>
> I am not a linux programmer and am using the obabel in a batch file (or
> the Open Babel GUI) when I try to convert smi files to 3d sdf format using
> Gen3d, I get a lot of error messages such as:
>
>
>
> I tried to find an explanation in your forum but did not understand what I
> found there.
>
> In addition, the 3d coordinates were quite terrible for many of the
> compounds that I calculated see attached file
>
> Expected structure
>
>
>
> Calculated structure
>
>
>
> Thanks, advance for your help,
>
> M. Ben-Tzion
>
>
>
> Dr. Moshe Ben-Tzion
>
> Department of Chemistry
>
> Bar-Ilan University, Ramat Gan 52900, Israel
>
> e-mail: ben...@biu.ac.il
>
> Website: http://ch.biu.ac.il/bentzion
>
> Tel: (03) 531-8305 Fax: 972-3-738-4053
>
> Cell:(054) 660-3310 Beeper: 88341(610-6666)
>
> =============================================
>
> In the beginning there was nothing and then G-d created light.
>
> And there was still nothing but you could see it better.
>
>
>
>
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