Questions tagged [openbabel]

Questions about or related to Open Babel.

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2 votes
0 answers

Autodock 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 script present in the mgltools ...
6 votes
1 answer

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 ...
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5 votes
0 answers

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 ...
15 votes
2 answers

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. ...
  • 15.1k
10 votes
2 answers

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 ...
  • 7,794