Adding Hydrogens

Previous Topic Next Topic
 
classic Classic list List threaded Threaded
3 messages Options
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Adding Hydrogens

Christopher Beeler

Hello, I am currently trying to use OpenBabel to add hydrogen to my XYZ molecules but it is not adding any. I am using version 2.3.2 on Linux. I have attached the input and output files. The command I am using is 'babel -ixyz molecule_1.xyz -oxyz molecule_1.in -h'. The output file should have 8 hydrogen now but it still contains 0.


Thank you-Chris Beeler, [hidden email]


------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
OpenBabel-discuss mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss

molecule_1.in (690 bytes) Download Attachment
molecule_1.xyz (244 bytes) Download Attachment
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: Adding Hydrogens

Noel O'Boyle
Administrator
"-h" is misnamed, I'm afraid. It doesn't add hydrogens to fill
valencies, but rather converrts implicit to explicit hydrogens. You
can open in Avogadro and click "Build/AddHydrogens" to do this.

Could I ask you where the XYZ file came from? It may be that a
different route might help.

Note to Geoff: would this be a useful 'op' or else option on XYZ?

- Noel

On 12 June 2017 at 16:22, Christopher Beeler <[hidden email]> wrote:

> Hello, I am currently trying to use OpenBabel to add hydrogen to my XYZ
> molecules but it is not adding any. I am using version 2.3.2 on Linux. I
> have attached the input and output files. The command I am using is 'babel
> -ixyz molecule_1.xyz -oxyz molecule_1.in -h'. The output file should have 8
> hydrogen now but it still contains 0.
>
>
> Thank you-Chris Beeler, [hidden email]
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> OpenBabel-discuss mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>

------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
OpenBabel-discuss mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: Adding Hydrogens

Geoff Hutchison
> "-h" is misnamed, I'm afraid. It doesn't add hydrogens to fill
> valencies, but rather converrts implicit to explicit hydrogens. You
> can open in Avogadro and click "Build/AddHydrogens" to do this.

Well, Avogadro will just call Open Babel. ;-)

> Note to Geoff: would this be a useful 'op' or else option on XYZ?

Maybe? It's probably more useful as an 'op' because there may be other files that come in with "missing hydrogens"

-G
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
OpenBabel-discuss mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Loading...