Questions tagged [openbabel]

Questions about or related to Open Babel.

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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". ...
Frank's user avatar
  • 195
6 votes
3 answers

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 ...
Meheret's user avatar
  • 93
6 votes
1 answer

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. ...
Camps's user avatar
  • 22.3k
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 ...
user3765252's user avatar
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 ...
Camps's user avatar
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5 votes
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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 ...
Julio Coll's user avatar
16 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. ...
Susi Lehtola's user avatar
11 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 ...
Cody Aldaz's user avatar
  • 7,957