Questions tagged [openbabel]
Questions about or related to Open Babel.
8
questions
5
votes
1
answer
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obabel error OpenAndSetFormat Cannot open
I'm trying to convert .xyz to .sdf with Open Babel on Ubuntu 22.04, but I am getting an error message "Cannot open orca.sdf".
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- 195
6
votes
3
answers
731
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Using OpenBabel's gen3d in a Python notebook
I want to preface this by saying I am really new to computational chemistry and this kind of programming in general, but I am having real trouble figuring out how to use OpenBabel's ...
- 93
6
votes
1
answer
285
views
Is it possible to recover the protein structure after conversions PDB->XYZ->PDB?
Let suppose that, for a given reason, a PDB file (with all the residues/chains/heteratom/cofactor/ligand information inside) is converted to a XYZ file. Doing that, all protein information is lost.
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- 22.3k
2
votes
0
answers
480
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Autodock prepare_receptor4.py script gives error while converting pdb files to pdbqt files
Cross-posted on Chemistry.SE.
I am trying to make pdbqt files from pdb files for Docking with Autodock vina but getting errors while running the prepare_receptor4.py script present in the mgltools ...
- 21
6
votes
1
answer
370
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Alternatives to OpenBabel for converting *large* files?
I have been using OpenBabel as a handy-tool for converting small files without any issues.
Now, I am working with graphene-like systems with hundreds or even ...
- 22.3k
5
votes
0
answers
151
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How can I add double bonds to Triazine-derivatives for OpenBabel generation of pdbqt files? [closed]
The double bonds are initially present at the sdf file but disappear or are misplaced after .pdbqt conversion. I tried all kinds of combinations using renumbering ...
- 51
16
votes
2
answers
816
views
What's the best quantum chemistry output parser for the command line?
This question is about tools like Open Babel. Are there any good command-line parsers for quantum chemistry program outputs? A good Python library could come in as a close second.
I am interested e.g. ...
- 18k
11
votes
2
answers
394
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How to canonicalize SMILES written with aromatic bond symbols (:)?
I am using a package called PySmiles and it is returning a dialect of SMILES for aromatic groups that uses aromatic bond symbols
e.g.
NC:1:N:N:C:[N]1N.
RDKit does ...
- 7,957