You can either take the original structure and rotate a random dihedral by
a random angle and continue, always using the original input for the random
dihedral rotation or you can use the previously randomized structure for
the input to the next random dihedral rotation.
The first option will not cause non-bonded cyclic structures to form, so if
you needed to see if a random structure could come in close contact to for
cycles, because it requires either a starting geometry in a U shape or you
have to torque multiple rotomers. If you start with a linear molecule, only
modifying the original structure will result in a bunch of V shaped
structures.
By the way the conformers look in the files I sent, I'm guessing openbabel
generates all "random" conformers from the original input and does not base
the next random conformer on the previously generated structure.
Hope this helps!
Carrie
On Wed, Nov 15, 2017 at 12:01 PM, Geoffrey Hutchison <
geoff.hutchi...@gmail.com> wrote:
> > Does obabel sample dihedral angles from the input file, or does it
> sample from the new dihedral angles?
>
>
> It samples from the initial geometry. What do you mean by "new dihedral
> angles?"
>
> The presumption of most conformer generation tools is that the set of
> rotatable bonds is fixed.
>
> -Geoff
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