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MM3 atom typing

Jan Halborg Jensen
Hi all

Can anyone tell me how to use the -3 keyword to get MM3 atom types?

For example

babel -isdf aceticacid.sdf -otxyz aceticacidmm3.txyz -3
babel -isdf aceticacid.sdf -otxyz -3 aceticacidmm3.txyz 

doesn’t seem to work, i.e. it gives me mm2 atom types.  For example the last atom type in txyz should be 24 as far as I can see.

I generated aceticacid.sdf by

obabel -:'CC(=O)O' -osdf --Gen3D > aceticacid.sdf

Best regards, Jan
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
Jan H. Jensen Professor
Department of Chemistry [hidden email]  
University of Copenhagen Phone: +45 51 82 69 85
Universitetsparken 5 FAX:   +45 35 32 02 14
2100 Copenhagen Denmark
Twitter: @janhjensen
http://molecularmodelingbasics.blogspot.com
http://proteinsandwavefunctions.blogspot.com/
http://compchemhighlights.org: A new kind of chemistry journal
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Re: MM3 atom typing

Noel O'Boyle
Administrator
Here you go: https://openbabel.org/docs/dev/FileFormats/Overview.html

On 18 May 2017 at 09:22, Jan Halborg Jensen <[hidden email]> wrote:

> Hi all
>
> Can anyone tell me how to use the -3 keyword to get MM3 atom types?
> https://openbabel.org/docs/dev/FileFormats/Tinker_XYZ_format.html
>
> For example
>
> babel -isdf aceticacid.sdf -otxyz aceticacidmm3.txyz -3
> babel -isdf aceticacid.sdf -otxyz -3 aceticacidmm3.txyz
>
> doesn’t seem to work, i.e. it gives me mm2 atom types.  For example the last
> atom type in txyz should be 24 as far as I can see.
>
> I generated aceticacid.sdf by
>
> obabel -:'CC(=O)O' -osdf --Gen3D > aceticacid.sdf
>
> Best regards, Jan
> =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
> Jan H. Jensen Professor
> Department of Chemistry [hidden email]
> University of Copenhagen Phone: +45 51 82 69 85
> Universitetsparken 5 FAX:   +45 35 32 02 14
> 2100 Copenhagen Denmark
> Twitter: @janhjensen
> http://molecularmodelingbasics.blogspot.com
> http://proteinsandwavefunctions.blogspot.com/
> http://compchemhighlights.org: A new kind of chemistry journal
> =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
>
>
> ------------------------------------------------------------------------------
> 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
>

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