Your molecule has a lot of rotatable bonds and the ability to easily clash
with itself. And you are generating very few potential conformations out of
the space (less than 1% of the space, or when you ask for 10,000 as in the
command, not your output, less than 0.1% of the space). For this molecule,
even at 1 million conformers, the default, all the produced conformers have
self-clashes that result in high energies outside the default energy cut
off. If you increase, rather than decrease, the number of conformers, to
the 13 million that it says is the whole space, you'll get thousands of
diverse conformers.
On Wed, Sep 6, 2017 at 11:13 AM, MD Simulation <mdsimulationgr...@gmail.com>
wrote:
> Hello,
>
> I'm using the most recent version of OpenBabel (2.4.1) on Windows.
>
> I am having trouble getting Confab to generate structures based on the
> attached structure. I am using the command:
>
> >>> obabel polymer.mol2 -O confs.mol2 --confab --conf 10000 --verbose
>
> This is the output:
>
> """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""
> """"""""""""""""""""""""""""
> **Starting Confab 1.1.0
> **To support, cite Journal of Cheminformatics, 2011, 3, 8.
> ..Input format = xyz
> ..Output format = sdf
> ..RMSD cutoff = 0.5
> ..Energy cutoff = 50
> ..Conformer cutoff = 100000
> ..Write input conformation? False
> ..Verbose? True
>
> **Molecule 1
> ..title = polymer.xyz
> ..number of rotatable bonds = 11
> ....rotor 1 from 42 to 85 has 5 values
> ....rotor 2 from 43 to 35 has 3 values
> ....rotor 3 from 43 to 36 has 3 values
> ....rotor 4 from 92 to 91 has 6 values
> ....rotor 5 from 80 to 91 has 6 values
> ....rotor 6 from 22 to 41 has 5 values
> ....rotor 7 from 72 to 74 has 5 values
> ....rotor 8 from 8 to 29 has 6 values
> ....rotor 9 from 67 to 69 has 3 values
> ....rotor 10 from 7 to 29 has 6 values
> ....rotor 11 from 68 to 67 has 3 values
> ..tot conformations = 13122000
> ....Using a cutoff of 100000 we will only explore 0.8% of these
> ..tot confs tested = 100000
> ..below energy threshold = 0
> ....tree size = 0 confs = 0
> ....new tree size = 0 confs = 0
> ..generated 0 conformers
>
> 0 molecules converted
> """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""
> """"""""""""""""""""""""""""""""
>
> As you can see from the output, nothing is generated.
>
> Any ideas to why Confab is not producing conformers?
>
> Thanks!
>
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