[Open Babel] Gasteiger charges

Previous Topic Next Topic
 
classic Classic list List threaded Threaded
7 messages Options
Reply | Threaded
Open this post in threaded view
|

[Open Babel] Gasteiger charges

Takayuki KOTANI
Hi all.

Is it possible to calculate Gasteiger charges such as positive charged
molecules or pyridine N-oxide?
I am using openbabel-1.100.0 under cygwin environment.


Takayuki KOTANI, Ph.D.

Nippon Zoki Pharmaceutical Co. Ltd.
Institute of Bio-Active Science (IBAS)

Phone +81-795-42-5500
Facsimile +81-795-42-5332
E-mail [hidden email]



-------------------------------------------------------
This SF.net email is sponsored by: Splunk Inc. Do you grep through log files
for problems?  Stop!  Download the new AJAX search engine that makes
searching your log files as easy as surfing the  web.  DOWNLOAD SPLUNK!
http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click
_______________________________________________
OpenBabel-discuss mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Reply | Threaded
Open this post in threaded view
|

Re: [Open Babel] Gasteiger charges

Geoffrey Hutchison

On Nov 25, 2005, at 9:17 AM, Takayuki KOTANI wrote:

> Is it possible to calculate Gasteiger charges such as positive charged
> molecules or pyridine N-oxide?

Is it possible? Sure. Is it correct? I don't know, I'd need some test  
molecules to compare the OB output to another program.

Sorry I can't be more specific towards your question, but it's a bit  
ambiguous. Yes, the OB code will produce Gasteiger sigma charges for  
such molecules.

Best regards,
-Geoff


-------------------------------------------------------
This SF.net email is sponsored by: Splunk Inc. Do you grep through log files
for problems?  Stop!  Download the new AJAX search engine that makes
searching your log files as easy as surfing the  web.  DOWNLOAD SPLUNK!
http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click
_______________________________________________
OpenBabel-discuss mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Reply | Threaded
Open this post in threaded view
|

Re: [Open Babel] Gasteiger charges

Geoffrey Hutchison
In reply to this post by Takayuki KOTANI

On Nov 28, 2005, at 8:59 AM, Takayuki KOTANI wrote:

> Is the command wrong? Gasteiger charge calculation used in OB is not
> compatible with Pyridine N-Oxide?
> Same situation was occurred at N-methylpyridinium ion.

Do you have a comparison for what the Gasteiger charge "should" be?  
The question I have is whether this is a bug in Open Babel, or a bad  
result for the Gasteiger sigma model. I'm not sure I've understood  
your messages. Do you want to know about Gasteiger charges in  
general? Or the charges calculated by OB?

Have you tried calculating Gasteiger charges using the same molecules  
in other code?

For example, sing the Gasteiger group's web service, asking for  
"Sigma charge PEOE" under atomic properties.
http://www2.chemie.uni-erlangen.de/services/petra/smiles.phtml

I tried pyridine-N-oxide (SMILES 'O=n1ccccc1')
I get -0.146 on the N.

I tried N-methylpyridinium (SMILES 'C[n+]1ccccc1')
I get -0.4142 on the N.

Yes, there seems to be some sort of "parameter creep" and it would be  
nice to verify our model against the Gasteiger group's code. But the  
way I've been reading your question, it sounds like you want to know  
about the Open Babel calculation. I think the OB code is calculating  
Gasteiger PEOE charges correctly given the published model and  
parameters.

> In addition, why mopac calculated charges were not imported to mol2  
> file?

That would be a bug. I'll take a look at your MOPAC file and see  
what's going on.

Cheers,
-Geoff


-------------------------------------------------------
This SF.net email is sponsored by: Splunk Inc. Do you grep through log files
for problems?  Stop!  Download the new AJAX search engine that makes
searching your log files as easy as surfing the  web.  DOWNLOAD SPLUNK!
http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click
_______________________________________________
OpenBabel-discuss mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Reply | Threaded
Open this post in threaded view
|

Re: [Open Babel] Gasteiger charges

Geoffrey Hutchison

On Nov 28, 2005, at 2:48 PM, Geoffrey Hutchison wrote:

> For example, sing the Gasteiger group's web service, asking for  
> "Sigma charge PEOE" under atomic properties.
> http://www2.chemie.uni-erlangen.de/services/petra/smiles.phtml
>
> I tried pyridine-N-oxide (SMILES 'O=n1ccccc1')
> I get -0.146 on the N.
>
> I tried N-methylpyridinium (SMILES 'C[n+]1ccccc1')
> I get -0.4142 on the N.

I just checked OB v2.0:
For pyridine-N-oxide:
I get -0.147 on the N.

For N-methylpyridinium:
I get -0.3562 on the N.

So there's definitely an error in the OB code for the calculated N-
methyl, but not in the N-oxide case.

Cheers,
-Geoff


-------------------------------------------------------
This SF.net email is sponsored by: Splunk Inc. Do you grep through log files
for problems?  Stop!  Download the new AJAX search engine that makes
searching your log files as easy as surfing the  web.  DOWNLOAD SPLUNK!
http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click
_______________________________________________
OpenBabel-discuss mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Reply | Threaded
Open this post in threaded view
|

RE: Gasteiger charges

Takayuki KOTANI
 
>I just checked OB v2.0:
>For pyridine-N-oxide:
>I get -0.147 on the N.

>For N-methylpyridinium:
>I get -0.3562 on the N.

>So there's definitely an error in the OB code for the calculated N- methyl,
but not in the N-oxide case.

>I tried pyridine-N-oxide (SMILES 'O=n1ccccc1') I get -0.146 on the N.

Since N atom on pyridine-N-oxide is cationic and O atom is anionic, SMILES
would be more likely '[O-][n+]1ccccc1' rather than 'O=n1ccccc1'.
I tried to calculate atomic charge of '[O-][n+]1ccccc1' at
http://www2.chemie.uni-erlangen.de/services/petra/smiles.phtml, the results
is similar with 'O=n1ccccc1'.
It is not the OB code problem, but these results show that pyridine-N-oxide
is not suitable to calculate Gasteiger charges?


>> In addition, why mopac calculated charges were not imported to mol2
>> file?
>That would be a bug. I'll take a look at your MOPAC file and see what's
going on.
I am looking forward  hearing your results. Thank you.

Regards

Takayuki KOTANI, Ph.D.




-------------------------------------------------------
This SF.net email is sponsored by: Splunk Inc. Do you grep through log files
for problems?  Stop!  Download the new AJAX search engine that makes
searching your log files as easy as surfing the  web.  DOWNLOAD SPLUNK!
http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click
_______________________________________________
OpenBabel-discuss mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Reply | Threaded
Open this post in threaded view
|

RE: Gasteiger charges

Takayuki KOTANI
In reply to this post by Takayuki KOTANI
>>> In addition, why mopac calculated charges were not imported to mol2
>>> file?
>>That would be a bug. I'll take a look at your MOPAC file and see what's
going on.
>I am looking forward  hearing your results. Thank you.

Today I downloaded and tried openbabel-2.0.0awin.
It works very well for importing mopac calculated charges to mol2 file.
I really appreciated since I could not make babel-2.0.0 on cygwin
environment.

Is it possible to make mol2 files from mopac output files with optionally
selection of Gasteiger charges?

Thanks in advance for any help!

Regards

Takayuki KOTANI, Ph.D.

-----Original Message-----
From: Takayuki KOTANI [mailto:[hidden email]]
Sent: Tuesday, November 29, 2005 9:38 PM
To: 'Geoffrey Hutchison'; '[hidden email]'
Subject: RE: [Open Babel] Gasteiger charges

 
>I just checked OB v2.0:
>For pyridine-N-oxide:
>I get -0.147 on the N.

>For N-methylpyridinium:
>I get -0.3562 on the N.

>So there's definitely an error in the OB code for the calculated N- methyl,
but not in the N-oxide case.

>I tried pyridine-N-oxide (SMILES 'O=n1ccccc1') I get -0.146 on the N.

Since N atom on pyridine-N-oxide is cationic and O atom is anionic, SMILES
would be more likely '[O-][n+]1ccccc1' rather than 'O=n1ccccc1'.
I tried to calculate atomic charge of '[O-][n+]1ccccc1' at
http://www2.chemie.uni-erlangen.de/services/petra/smiles.phtml, the results
is similar with 'O=n1ccccc1'.
It is not the OB code problem, but these results show that pyridine-N-oxide
is not suitable to calculate Gasteiger charges?


>> In addition, why mopac calculated charges were not imported to mol2
>> file?
>That would be a bug. I'll take a look at your MOPAC file and see what's
going on.
I am looking forward  hearing your results. Thank you.

Regards

Takayuki KOTANI, Ph.D.



-------------------------------------------------------
This SF.net email is sponsored by: Splunk Inc. Do you grep through log files
for problems?  Stop!  Download the new AJAX search engine that makes
searching your log files as easy as surfing the  web.  DOWNLOAD SPLUNK!
http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click
_______________________________________________
OpenBabel-discuss mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Reply | Threaded
Open this post in threaded view
|

Re: Gasteiger charges

Geoffrey Hutchison

On Nov 29, 2005, at 8:42 PM, Takayuki KOTANI wrote:

> I really appreciated since I could not make babel-2.0.0 on cygwin
> environment.

Yes, that's an unfortunate problem right now. I think I know how to  
solve it, but it may take a few days due to other work.

> Is it possible to make mol2 files from mopac output files with  
> optionally
> selection of Gasteiger charges?

Oh, that's a great suggestion, thanks!

Thanks for your suggestions and reports, they were quite helpful.

Cheers,
-Geoff



-------------------------------------------------------
This SF.net email is sponsored by: Splunk Inc. Do you grep through log files
for problems?  Stop!  Download the new AJAX search engine that makes
searching your log files as easy as surfing the  web.  DOWNLOAD SPLUNK!
http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click
_______________________________________________
OpenBabel-discuss mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss