Faculty for Chemistry and Pharmacy - Group of Prof. Zipse
 

OpenBabel

The program obabel is the command line version of Open Babel. Much of the relevant background has been described by G. R. Hutchison et al. in the Journal of Chemoinformatics 2011, 3, article 33. The program is very useful for the interconversion of molecular structures between different file formats popular in computational chemistry and molecular modeling. Format conversions are performed from the command line with the command:

obabel [-i<input-ID>] infile [-o<output-ID>] [-O outfile] [OPTIONS]

where "-i<input-ID>" defines the format of the file named "infile" that contains some molecular structure information. Reading from a Gaussian 09 output file, for example, the input-ID equates to "-ig09". The format to which this structural information will be converted to is given by the "-o<output-ID>" qualifier, and the converted structure will be written to the file given after "-O". For the sake of example let us assume that we have performed a geometry optimization with Gaussian 09, the resulting output file being "rad004.log". The command:

obabel -ig09 rad004.log -ogjf -O rad004.gjf

will extract the last (that is, the optimized) geometry in this output file and write the coordinates to the new file "rad004.gjf" in the input file format for Gaussian 09. This works in a completely analogous manner for output files of MOLPRO and ORCA, the required input and output qualifiers being:

input-ID options
-iorca (ORCA output files)
-isdf
-ig09 (Gaussian 09 output file)
-ig16 (Gaussian 16 output file)
-impo (MOLPRO output file)

output-ID options
-oorcainp (ORCA input files)
-osdf
-ogjf (Gaussian input file)
-ocom (Gaussian input file)
-omp (MOLPRO input file)

One very practical file format for the transfer and storage of structural information is the sdf file format generated with the "-osdf" output qualifier. This file format can be read by GaussView and molden, and also by desktop programs such as ChemDraw. It can also be used to combine several structures into a single file in the sense of generating an ordered list of the conformers of a given system. So let us assume that you have found three different conformers of the same system located in the Gaussian 09 output files but_025sp2.log, but_022sp2.log, and but_010sp2.log (with increasing relative energy). The obabel command:

obabel -ig09 but_025sp2.log but_022sp2.log but_010sp2.log -osdf -O but_ordered_list.sdf

will then generate the new file "but_ordered_list.sdf" with the structures of the individual conformers listed by increasing energy in the sdf format. Opening this file with GaussView or molden presents you with a popup window, where all individual entries of the sdf file are shown in the correct order and their original file names, and from where single structures can now be selected for further inspection.

The best source for further information and program documentation (version 3.0.0) can be found at:
https://open-babel.readthedocs.io/en/latest/Command-line_tools/babel.html
and a list of supported file formats can be found at:
https://open-babel.readthedocs.io/en/latest/FileFormats/Overview.html#file-formats

A (printable) documentation file can be found at:
https://buildmedia.readthedocs.org/media/pdf/open-babel/latest/open-babel.pdf