[Open Babel] Cant activate Confab

[alfredoq]

Dear OBabel user: I have been struggling to activate the Confab module of
obabel for several day without any luck. I compiled Open Babel 2.3.2,
installed all the required libraries (including EIGEN) as mentioned in the
provided INSTALL file, and carefully followed all the instructions. After
compilation all test passed succesfully. However, the outcome of 

obabel -L confab

gives: "confab is not a recognized plugin type"


Any hint on how to solve this issue?

Thank you very much in advance for the support,

best regards

Alfredo



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Re: [Open Babel] question regarding error messages and poor results

[Tim Vandermeersch]

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"  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-)
>
> =
>
> 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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Re: [Open Babel] question regarding error messages and poor results

[Andreas Kempe]

obabel is looking for data files that contain atom definitions, force 
field parameters and so on.
You need to set the enviroment variable BABEL_DATADIR either globally or 
in your batch file, e.g. add

set BABEL_DATADIR=C:\ProgramData\OpenBabel-2.3.1\data

The directory might be different on your system. So simply search for 
UFF.prm and set the variable accordingly.


Best regards
Andreas



 Original-Nachricht 
Betreff: [Open Babel] question regarding error messages and poor results
Von: Moshe Ben-zion 
An: openbabel-disc...@lists.sf.net 
Datum: 25.02.2016 11:23


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-)

=

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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