Assuming that you compiled it in the first place, you need to
recompile after installing Eigen.
- Noel
On 29 September 2016 at 11:44, Samdani A wrote:
> Thank you Noel.
>
> Should I reinstall obabel again after installing Eigen?
>
> On Thu, Sep 29, 2016 at 4:06 PM, Noel O'Boyle wrote:
>>
>> Eig
Eigen2 or 3 is required for the conformer operations. See the docs
(http://openbabel.org/docs/current/Installation/install.html#requirements)
although it needs some updating.
- Noel
On 29 September 2016 at 11:23, samdani wrote:
> Hi all,
>
> I had recently installed obabel-2.4.0 and trying to ge
> This gives me a file with only one 3D structure, which is actually the one
> obtained from the gen3d option. For some reason no conformers are generated.
> I also tried the FF derived searches at no success.
IIRC, you can't perform both the gen3d and the conformer search in one step
from the
> But when I try to generate conformers using:
>
> obabel ./astex_1g9v/ligand_babel3d.sdf -O/tmp/test.sdf --conformer --nconf 10
> --writeconformers --score rmsd
>
> I get:
>
> Initial conformer does not pass filter!
> Initial conformer count: 0
> Generation #1 0
> Generation #2 -nan
Yes, th
On 31 May 2012 03:56, Geoff Hutchison wrote:
>
> On May 29, 2012, at 11:23 AM, JP wrote:
>
> > This value of 1A in the steric filter is not available from the command
> line, correct?
>
> No, there isn't (yet) a way to set that. The current SVN trunk now has an
> improved filter. It considers hyd
On May 29, 2012, at 11:23 AM, JP wrote:
> This value of 1A in the steric filter is not available from the command line,
> correct?
No, there isn't (yet) a way to set that. The current SVN trunk now has an
improved filter. It considers hydrogens, and will also filter based on VdW
radii for eac
On 29 May 2012 15:25, Geoff Hutchison wrote:
> Some of the generated conformers look really ugly (in terms of close
> atoms/steric clashes).
> I have placed a selected subset at: http://imgur.com/a/LgJqL
>
> Is that to be expected in RMSD scoring -- because I have not used --score
> energy? (I tr
> Some of the generated conformers look really ugly (in terms of close
> atoms/steric clashes).
> I have placed a selected subset at: http://imgur.com/a/LgJqL
>
> Is that to be expected in RMSD scoring -- because I have not used --score
> energy? (I tried the energy scoring, and the molecules
