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errors in --gen3d #2676
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@cassguff Based on the documentation flag
is sufficient for (this example) to generate a conformer of pyridine (including protons for pH 7.4) written into file |
The bigger problem is that it's reporting it cannot find any of the force field data files. You didn't mention how you installed it, but that's the key problem. The install can't find any files needed for coordinate generation. |
I installed it by simply just downloading the latest version of the 64 bit
binary installer.
Thanks for also pointing out that -b is not needed for this command.
…On Wed, Feb 28, 2024 at 10:43 AM nbehrnd ***@***.***> wrote:
Yeah,
https://open-babel.readthedocs.io/en/latest/Installation/install.html
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Is there a different way I should download and install?
On Wed, Feb 28, 2024 at 10:53 AM Cassandra Guffey ***@***.***>
wrote:
… I installed it by simply just downloading the latest version of the 64 bit
binary installer.
Thanks for also pointing out that -b is not needed for this command.
On Wed, Feb 28, 2024 at 10:43 AM nbehrnd ***@***.***> wrote:
> Yeah,
> https://open-babel.readthedocs.io/en/latest/Installation/install.html
>
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Re executables: with Windows 64bit in hand, you might i) deinstall the current installation of openbabel (for 64bit) to ii) then try the installer for 32bit. No guarantee this then works better. Else, openbabel is packaged for a couple of Linuxes. At least Debian, Ubuntu, and Fedora offer live images, i.e. the OS works from the RAM/without permanent installation on the hard disk, while accessing their openbabel package from the corresponding repositories -- just in case you don't want/are not permitted to modify the computer you use. If the structure isn't IP, you may consider cheminfo.org with its online instance of openbabel. It equally allows the conversion of e.g., a SMILES string into a 3D .sdf. |
It didn't work to do the 32 bit installer. I can just use Linux or the
online instance. Thanks.
…On Fri, Mar 1, 2024 at 9:12 AM nbehrnd ***@***.***> wrote:
Re executables: with Windows 64bit in hand, you might i) deinstall the
current installation of openbabel (for 64bit) to ii) then try the installer
for 32bit. No guarantee this then works better.
Else, openbabel is packaged for a couple of Linuxes. At least Debian,
Ubuntu, and Fedora offer live images, i.e. the OS works from the
RAM/without permanent installation on the hard disk, while accessing their
openbabel package from the corresponding repositories -- just in case you
don't want/are not permitted to modify the computer you use.
[image: Packaging status]
<https://repology.org/project/openbabel/versions>
If the structure isn't IP, you may consider cheminfo.org
<https://www.cheminfo.org/Chemistry/Cheminformatics/FormatConverter/index.html>
with its online instance of openbabel. It equally allows the conversion of
e.g., a SMILES string into a 3D .sdf.
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Environment Information
Open Babel version: Open Babel 3.1.1
Operating system and version: Windows 11
Expected Behavior
I'm just trying to convert a SMILES string to an .xyz file using the --gen3d to get an approximate low energy conformation. I expect to get an xyz file with 3d coordinates.
Actual Behavior
It generates the xyz file, but I do not get 3D coordinates ( in that the z column is all 0s) showing that no optimization is happening. I get the following output:==============================
*** Open Babel Error in OpenBabel::OBBuilder::LoadFragments
Cannot open ring-fragments-index.txt
*** Open Babel Error in OpenBabel::OBForceFieldMMFF94::ParseParamFile
Cannot open parameter file
*** Open Babel Error in OpenBabel::OBForceFieldUFF::ParseParamFile
Cannot open UFF.prm
*** Open Babel Error in OpenBabel::OBForceFieldUFF::SetTypes
Cannot open UFF.prm
1 molecule converted
Steps to Reproduce
I am using the command 'obabel -:"CCCC" -O 1.xyz --gen3D -xb -h' in the command line.
I saw a different thread about someone who added BABEL_DATADIR as an environment variable and fixing a similar problem, but that didn't work for me.
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