Partial charge on OSX system

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Partial charge on OSX system

Guoyi Li
Hi,

I installed the recommend 'ilabel' on my OSX system. I would like to use openbabel to generate the partial charge of my molecules. I could use the mmff partial charge method. But I still need to use qeq method. But it shows system could not find qeq. 

My workmate uses openbabel on his windows system and it works for him. I am wondering that could you please show me a way to implement qeq partial charge on my Macbook.

Thanks,


--
Guoyi Li
Graduate Research Associate
School for Engineering of Matter, Transport and Energy

Adaptive Intelligent Materials & Systems (AIMS) Center

http://aims.engineering.asu.edu/

Arizona State University

P.O. Box 876106

Tempe, AZ 85287-6106


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Re: Partial charge on OSX system

Geoff Hutchison
 I would like to use openbabel to generate the partial charge of my molecules. I could use the mmff partial charge method. But I still need to use qeq method. But it shows system could not find qeq. 

What version of Open Babel did you install? Can you give more specifics on "shows system could not find qeq"?

This is on my MacBook (running 10.10.x):

[ghutchis@Alumina] mol2: obabel -L charges
eem    Assign Electronegativity Equilization Method (EEM) atomic partial charges
eqeq    Assign EQEq (charge equilibration) partial charges.
gasteiger    Assign Gasteiger-Marsili sigma partial charges
mmff94       Assign MMFF94 partial charges
none    Clear all partial charges
qeq    Assign QEq (charge equilibration) partial charges (Rappe and Goddard, 1991)
qtpie    Assign QTPIE (charge transfer, polarization and equilibration) partial charges (Chen and Martinez, 2007)


Cheers,
-Geoff

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Re: Partial charge on OSX system

Geoff Hutchison
Please don't e-mail me directly. I'm sure others could answer your question on the mailing list - it's why it exists.

I don't know what you mean by "linux" version. Do you mean you compiled from source code?

Also, I don't know what you mean by "openbabel didn't work" since presumably if you were able to use "obabel" to generate qeq charges, it worked.

Please be more specific. What error messages do you have? What programs are you trying to use?

Best regards,
-Geoff


On Jul 5, 2015, at 8:49 PM, Guoyi Li <[hidden email]> wrote:

Hi Geoffrey,

I am sorry disturbing you again. 

Could you please let me know how did you download and install your openbabel? I tried using linux version and I got the qeq. But the openbabel didn't work. Could you please give me the link or procedure you used? Thank you!

Sincerely,

On Sun, Jul 5, 2015 at 3:38 PM, Geoffrey Hutchison <[hidden email]> wrote:
 I would like to use openbabel to generate the partial charge of my molecules. I could use the mmff partial charge method. But I still need to use qeq method. But it shows system could not find qeq. 

What version of Open Babel did you install? Can you give more specifics on "shows system could not find qeq"?

This is on my MacBook (running 10.10.x):

[ghutchis@Alumina] mol2: obabel -L charges
eem    Assign Electronegativity Equilization Method (EEM) atomic partial charges
eqeq    Assign EQEq (charge equilibration) partial charges.
gasteiger    Assign Gasteiger-Marsili sigma partial charges
mmff94       Assign MMFF94 partial charges
none    Clear all partial charges
qeq    Assign QEq (charge equilibration) partial charges (Rappe and Goddard, 1991)
qtpie    Assign QTPIE (charge transfer, polarization and equilibration) partial charges (Chen and Martinez, 2007)


Cheers,
-Geoff



--
Guoyi Li
Graduate Research Associate
School for Engineering of Matter, Transport and Energy
Adaptive Intelligent Materials & Systems (AIMS) Center
Arizona State University
P.O. Box 876106
Tempe, AZ 85287-6106


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Re: Partial charge on OSX system

David Hall
In reply to this post by Guoyi Li
As far as I know, the current ibabel ( http://www.macinchem.org/ibabel/ibabel3.php ) requires that you install openbabel first. Have you checked that the command line openbabel has the qeq charges?

-David


On Jul 3, 2015, at 1:34 AM, Guoyi Li <[hidden email]> wrote:

Hi,

I installed the recommend 'ilabel' on my OSX system. I would like to use openbabel to generate the partial charge of my molecules. I could use the mmff partial charge method. But I still need to use qeq method. But it shows system could not find qeq. 

My workmate uses openbabel on his windows system and it works for him. I am wondering that could you please show me a way to implement qeq partial charge on my Macbook.

Thanks,


--
Guoyi Li
Graduate Research Associate
School for Engineering of Matter, Transport and Energy
Adaptive Intelligent Materials & Systems (AIMS) Center
Arizona State University
P.O. Box 876106
Tempe, AZ 85287-6106
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you need to offload your IT needs and focus on growing your business.
Configured For All Businesses. Start Your Cloud Today.
https://www.gigenetcloud.com/_______________________________________________
OpenBabel-discuss mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss


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