question regarding error messages and poor results

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question regarding error messages and poor results

Moshe Ben-zion

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: [hidden email]

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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Re: 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 [hidden email]
An: [hidden email] [hidden email]
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: [hidden email]

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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Re: question regarding error messages and poor results

Tim Vandermeersch
In reply to this post by Moshe Ben-zion

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" <[hidden email]> 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: [hidden email]

Website: http://ch.biu.ac.il/bentzion

Tel: <a href="tel:%2803%29%20531-8305" value="+3235318305" target="_blank">(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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Re: question regarding error messages and poor results

Andreas Kempe
In reply to this post by Andreas Kempe
Ah, ok. For OpenBabel 2.3.2 the location of the data directory reads
%appdata%\OpenBabel-2.3.2\data
or the long form
C:\Users\<username>\AppData\Roaming\OpenBabel-2.3.2\data
I assume that you could not find UFF.prm the files as AppData is a hidden directory.

Best regards
Andreas

-------- Original-Nachricht --------
Betreff: Re: [Open Babel] question regarding error messages and poor results
Von: Moshe Ben-zion [hidden email]
An: Andreas Kempe [hidden email]
Datum: 28.02.2016 10:08

Dear Andreas,

          Apparently when I installed OpenBabel 2.3.2, the additional directory and file(s) did not get installed. I have no OpenBabel directory in my ProgramData directory and no UFF.prm anywhere on my computer. How does one go about correcting this?

All the best,

Moshe

 

From: Andreas Kempe [[hidden email]]
Sent: Friday, February 26, 2016 3:57 PM
To: Moshe Ben-zion [hidden email]; [hidden email]
Subject: Re: [Open Babel] question regarding error messages and poor results

 

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 [hidden email]
An: [hidden email] [hidden email]
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: [hidden email]

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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