Dear all, QEq partial charge predicts all zero value. Any suggestions ?

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

Dear all, QEq partial charge predicts all zero value. Any suggestions ?

peter308
Dear all
I am a newbie to openbabel. I am recently interested in QEq methods which can calculate partial charge based upon a certain input geometry. However i try to use a command which i found in the internet "babel -imol Au12.mol -omol2 Au12.mol2 --partialcharge qeq", but the result in Au12.mol2 shows partial charge on atoms are all zero. I am wondering are there some steps overlooked by me or is it the correct result predicted by Qeq method? It seems to me the results not physically reasonable because for clusters it shall be some charge dispersion which the numerical value might be small but can't be all zero. I wonder if the developer or users can test it for me and see if it is my problem or not ? Your kindness is much appreciated. I shall provide the Au12.mol file for your convenience.  

               
                                                                                  Best Peter



the Au12.mol start from the next line

  pot=  -957.376867514455
 OpenBabel11251612193D

 12 28  0  0  0  0  0  0  0  0999 V2000
    0.6152   -1.2671    0.9866 Au  0  0  0  0  0  0  0  0  0  0  0  0
   -0.6152    1.2671    0.9866 Au  0  0  0  0  0  0  0  0  0  0  0  0
    1.2737    0.6332    2.9883 Au  0  0  2  0  0  0  0  0  0  0  0  0
    1.8568   -0.7339   -1.3991 Au  0  0  0  0  0  0  0  0  0  0  0  0
    0.5769    1.8484   -1.4181 Au  0  0  0  0  0  0  0  0  0  0  0  0
    2.3882    1.1620    0.6557 Au  0  0  0  0  0  0  0  0  0  0  0  0
    3.2852    1.5796   -1.8587 Au  0  0  0  0  0  0  0  0  0  0  0  0
   -3.2852   -1.5796   -1.8587 Au  0  0  0  0  0  0  0  0  0  0  0  0
   -2.3882   -1.1620    0.6557 Au  0  0  0  0  0  0  0  0  0  0  0  0
   -1.8568    0.7339   -1.3991 Au  0  0  0  0  0  0  0  0  0  0  0  0
   -1.2737   -0.6332    2.9883 Au  0  0  2  0  0  0  0  0  0  0  0  0
   -0.5769   -1.8484   -1.4181 Au  0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1 11  1  0  0  0  0
  2  3  1  0  0  0  0
  2 11  1  0  0  0  0
  3 11  1  1  0  0  0
  4  6  1  0  0  0  0
  4  1  1  0  0  0  0
  5  4  1  0  0  0  0
  5 10  1  0  0  0  0
  5  6  1  0  0  0  0
  5  2  1  0  0  0  0
  6  2  1  0  0  0  0
  6  3  1  0  0  0  0
  7  5  1  0  0  0  0
  7  4  1  0  0  0  0
  7  6  1  0  0  0  0
  8 12  1  0  0  0  0
  8 10  1  0  0  0  0
  8  9  1  0  0  0  0
  9  1  1  0  0  0  0
 10  9  1  0  0  0  0
 10  2  1  0  0  0  0
 11  9  1  1  0  0  0
 12  4  1  0  0  0  0
 12 10  1  0  0  0  0
 12  9  1  0  0  0  0
 12  1  1  0  0  0  0
M  END
~
Reply | Threaded
Open this post in threaded view
|

Re: Dear all, QEq partial charge predicts all zero value. Any suggestions ?

Geoff Hutchison
Dear Peter,

I haven't looked in detail into the QEq implementation, but these methods derive in part due to equalizing electronegativity across a molecule (or in your case, cluster). Since there does not seem to be a difference in electronegativity between any of the Au atoms, I don't believe there should be any assigned partial charges.

Now, you might say "oh, but if I run a quantum calculation, I'll get different partial charges" and that's undoubtedly true.

Moreover, if you added ligands, you'd suddenly see charges pop up, since e.g., sulfur has different electronegativity than the Au, etc.

Hope that helps,
-Geoff



> Dear all
> I am a newbie to openbabel. I am recently interested in QEq methods which
> can calculate partial charge based upon a certain input geometry. However i
> try to use a command which i found in the internet "babel -imol Au12.mol
> -omol2 Au12.mol2 --partialcharge qeq", but the result in Au12.mol2 shows
> partial charge on atoms are all zero. I am wondering are there some steps
> overlooked by me or is it the correct result predicted by Qeq method? It
> seems to me the results not physically reasonable because for clusters it
> shall be some charge dispersion which the numerical value might be small but
> can't be all zero. I wonder if the developer or users can test it for me and
> see if it is my problem or not ? Your kindness is much appreciated. I shall
> provide the Au12.mol file for your convenience.  
>
>
>
> Best Peter
>
>
>
> the Au12.mol start from the next line
>
>  pot=  -957.376867514455
> OpenBabel11251612193D
>
> 12 28  0  0  0  0  0  0  0  0999 V2000
>    0.6152   -1.2671    0.9866 Au  0  0  0  0  0  0  0  0  0  0  0  0
>   -0.6152    1.2671    0.9866 Au  0  0  0  0  0  0  0  0  0  0  0  0
>    1.2737    0.6332    2.9883 Au  0  0  2  0  0  0  0  0  0  0  0  0
>    1.8568   -0.7339   -1.3991 Au  0  0  0  0  0  0  0  0  0  0  0  0
>    0.5769    1.8484   -1.4181 Au  0  0  0  0  0  0  0  0  0  0  0  0
>    2.3882    1.1620    0.6557 Au  0  0  0  0  0  0  0  0  0  0  0  0
>    3.2852    1.5796   -1.8587 Au  0  0  0  0  0  0  0  0  0  0  0  0
>   -3.2852   -1.5796   -1.8587 Au  0  0  0  0  0  0  0  0  0  0  0  0
>   -2.3882   -1.1620    0.6557 Au  0  0  0  0  0  0  0  0  0  0  0  0
>   -1.8568    0.7339   -1.3991 Au  0  0  0  0  0  0  0  0  0  0  0  0
>   -1.2737   -0.6332    2.9883 Au  0  0  2  0  0  0  0  0  0  0  0  0
>   -0.5769   -1.8484   -1.4181 Au  0  0  0  0  0  0  0  0  0  0  0  0
>  1  2  1  0  0  0  0
>  1  3  1  0  0  0  0
>  1 11  1  0  0  0  0
>  2  3  1  0  0  0  0
>  2 11  1  0  0  0  0
>  3 11  1  1  0  0  0
>  4  6  1  0  0  0  0
>  4  1  1  0  0  0  0
>  5  4  1  0  0  0  0
>  5 10  1  0  0  0  0
>  5  6  1  0  0  0  0
>  5  2  1  0  0  0  0
>  6  2  1  0  0  0  0
>  6  3  1  0  0  0  0
>  7  5  1  0  0  0  0
>  7  4  1  0  0  0  0
>  7  6  1  0  0  0  0
>  8 12  1  0  0  0  0
>  8 10  1  0  0  0  0
>  8  9  1  0  0  0  0
>  9  1  1  0  0  0  0
> 10  9  1  0  0  0  0
> 10  2  1  0  0  0  0
> 11  9  1  1  0  0  0
> 12  4  1  0  0  0  0
> 12 10  1  0  0  0  0
> 12  9  1  0  0  0  0
> 12  1  1  0  0  0  0
> M  END
> ~
>
>
>
>
> --
> View this message in context: http://forums.openbabel.org/Dear-all-QEq-partial-charge-predicts-all-zero-value-Any-suggestions-tp4659609.html
> Sent from the General discussion mailing list archive at Nabble.com.
>
> ------------------------------------------------------------------------------
> _______________________________________________
> OpenBabel-discuss mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss


------------------------------------------------------------------------------
_______________________________________________
OpenBabel-discuss mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss