Hello,
I would like to generate conformers with constrained core fragment as
fast as possible. I found this gist -
https://gist.github.com/kylebarlow/1756ea399ba6bfee3c2d3d054c17c3a3 - it
works as expected. One can supply a molecules and ids of moveable atom
and get a set of conformers. I rea
__ UPDATE: Changed to simple text-mail for readability
Hello Community!
I am using openbabel for conformer generation - my (intended) workflow is:
Guess a rough geometry using --gen3d, perform a weighted rotor search (obabel
with --conformer --weighted etc.), take the lowest energy conformer
Hello Community!
I am using openbabel for conformer generation - my (intended) workflow is:
Guess a rough geometry using --gen3d, perform a weighted rotor search (obabel with --conformer --weighted etc.), take the lowest energy conformer and optimize with obminimize.
I understand, tha
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
Hi all,
I had recently installed obabel-2.4.0 and trying to generate conformer for a
molecule. The --conformer flag when I used didn't generate any conformations
and produced single molecule file.
obabel test.mol2 -O ga_conf.mol2 --conformer --nconf 10 --writeconformers
1 molecule converted
And
> 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
Taking this smiles as input:
O[C@H]1[C@@H](OC2=CC(O)=CC(O)=C2C1=O)C1=CC=C(O)C(O)=C1
I tried to generate some conformers using this line:
obabel input.smi -O conformers.sdf --gen3D --conformer --nconf 4
This gives me a file with only one 3D structure, which is actually the one
obtained from the
Taking this smiles as input:
O[C@H]1[C@@H](OC2=CC(O)=CC(O)=C2C1=O)C1=CC=C(O)C(O)=C1
I tried to generate some conformers using this line:
obabel input.smi -O conformers.sdf --gen3D --conformer --nconf 4
This gives me a file with only one 3D structure, which is actually the one
obtained 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
Hi there,
I have checked out and successfully built openbabel from the svn repository
(trunk).
$ obabel -V
Open Babel 2.3.90 -- Jun 30 2012 -- 12:38:05
But when I try to generate conformers using:
obabel ./astex_1g9v/ligand_babel3d.sdf -O/tmp/test.sdf --conformer --nconf
10 --writeconformers --
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
Hi there OpenBabels!
I am generating conformers for
molecule C(=O)(O)C(C)(C)Oc1ccc(cc1)CC(=O)Nc1cc(cc(c1)C)C using the
--conformer option (and --writeconformers, otherwise I get only one
conformer written to file) in the following manner :-
obabel ligand_babel3d.sdf -O conf2.sdf --conformer --nco
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