using openbabel from github
Confab requires a 3D molecule as input, so I generate a 3D sdf of butane and
feed it into confab, which generates 2 conformers, the anti- and one of the
gauche- conformers. (If you loosen up the RMSD criteria, the other gauche
conformer is the third below the energy threshold and it will be kept)
-David
$ obabel -:'CCCC' -osdf --gen3D | obabel -isdf -osdf --confab
1 molecule converted
**Starting Confab 1.1.0
**To support, cite Journal of Cheminformatics, 2011, 3, 8.
..Input format = sdf
..Output format = sdf
..RMSD cutoff = 0.5
..Energy cutoff = 50
..Conformer cutoff = 1000000
..Write input conformation? False
..Verbose? False
**Molecule 1
..title =
..number of rotatable bonds = 1
..tot conformations = 3
..tot confs tested = 3
..below energy threshold = 3
..generated 2 conformers
OpenBabel01081510383D
14 13 0 0 0 0 0 0 0 0999 V2000
0.8992 0.0249 0.0552 C 0 0 0 0 0 0 0 0 0 0 0 0
2.4194 0.0362 0.0458 C 0 0 0 0 0 0 0 0 0 0 0 0
2.9653 1.1597 -0.8332 C 0 0 0 0 0 0 0 0 0 0 0 0
4.4855 1.1715 -0.8419 C 0 0 0 0 0 0 0 0 0 0 0 0
0.5301 -0.7866 0.6902 H 0 0 0 0 0 0 0 0 0 0 0 0
0.5017 -0.1256 -0.9536 H 0 0 0 0 0 0 0 0 0 0 0 0
0.5022 0.9680 0.4441 H 0 0 0 0 0 0 0 0 0 0 0 0
2.7840 -0.9317 -0.3175 H 0 0 0 0 0 0 0 0 0 0 0 0
2.7846 0.1555 1.0725 H 0 0 0 0 0 0 0 0 0 0 0 0
2.6000 2.1275 -0.4704 H 0 0 0 0 0 0 0 0 0 0 0 0
2.6007 1.0399 -1.8601 H 0 0 0 0 0 0 0 0 0 0 0 0
4.8825 1.3222 0.1671 H 0 0 0 0 0 0 0 0 0 0 0 0
4.8546 1.9831 -1.4768 H 0 0 0 0 0 0 0 0 0 0 0 0
4.8830 0.2286 -1.2306 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 5 1 0 0 0 0
1 6 1 0 0 0 0
1 7 1 0 0 0 0
2 3 1 0 0 0 0
2 8 1 0 0 0 0
2 9 1 0 0 0 0
3 4 1 0 0 0 0
3 10 1 0 0 0 0
3 11 1 0 0 0 0
4 12 1 0 0 0 0
4 13 1 0 0 0 0
4 14 1 0 0 0 0
M END
$$$$
OpenBabel01081510383D
14 13 0 0 0 0 0 0 0 0999 V2000
0.8992 0.0249 0.0552 C 0 0 0 0 0 0 0 0 0 0 0 0
2.4194 0.0362 0.0458 C 0 0 0 0 0 0 0 0 0 0 0 0
2.9653 1.1597 -0.8332 C 0 0 0 0 0 0 0 0 0 0 0 0
2.5035 2.5234 -0.3450 C 0 0 0 0 0 0 0 0 0 0 0 0
0.5301 -0.7866 0.6902 H 0 0 0 0 0 0 0 0 0 0 0 0
0.5017 -0.1256 -0.9536 H 0 0 0 0 0 0 0 0 0 0 0 0
0.5022 0.9680 0.4441 H 0 0 0 0 0 0 0 0 0 0 0 0
2.7840 -0.9317 -0.3175 H 0 0 0 0 0 0 0 0 0 0 0 0
2.7846 0.1555 1.0725 H 0 0 0 0 0 0 0 0 0 0 0 0
2.6342 1.0171 -1.8684 H 0 0 0 0 0 0 0 0 0 0 0 0
4.0612 1.1311 -0.8365 H 0 0 0 0 0 0 0 0 0 0 0 0
1.4113 2.5964 -0.3601 H 0 0 0 0 0 0 0 0 0 0 0 0
2.9055 3.3124 -0.9882 H 0 0 0 0 0 0 0 0 0 0 0 0
2.8466 2.7109 0.6775 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 5 1 0 0 0 0
1 6 1 0 0 0 0
1 7 1 0 0 0 0
2 3 1 0 0 0 0
2 8 1 0 0 0 0
2 9 1 0 0 0 0
3 4 1 0 0 0 0
3 10 1 0 0 0 0
3 11 1 0 0 0 0
4 12 1 0 0 0 0
4 13 1 0 0 0 0
4 14 1 0 0 0 0
M END
$$$$
> On Jan 7, 2015, at 10:44 AM, Ben Albrecht <benalbr...@gmail.com> wrote:
>
> I am struggling to find a working example of the openbabel confab conformer
> search algorithm. I documented my experiences with it in this bug report.
> <https://sourceforge.net/p/openbabel/bugs/950/>
>
> Could someone post an input command and input file for a working case of
> confab? An openbabel version number would be useful as well.
>
> Thanks,
>
> Ben Albrecht
> ------------------------------------------------------------------------------
> Dive into the World of Parallel Programming! The Go Parallel Website,
> sponsored by Intel and developed in partnership with Slashdot Media, is your
> hub for all things parallel software development, from weekly thought
> leadership blogs to news, videos, case studies, tutorials and more. Take a
> look and join the conversation now.
> http://goparallel.sourceforge.net_______________________________________________
> OpenBabel-discuss mailing list
> OpenBabel-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
------------------------------------------------------------------------------
Dive into the World of Parallel Programming! The Go Parallel Website,
sponsored by Intel and developed in partnership with Slashdot Media, is your
hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now. http://goparallel.sourceforge.net
_______________________________________________
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
