Converting Structure File Formats

Jaguar uses the OpenBabel program [26] to convert between many of the file formats used in computational chemistry. Babel can read over 40 kinds of input and output file types, and writes both cartesian and Z-matrix geometry specifications. Babel is used in the GUI to read and write files that are not in Jaguar or Maestro format. You can also request Jaguar to write out files during a job run using the babel or babelg keywords (see File Format Conversion Keywords in the Jaguar Input File for more information).

To convert file formats from the command line, you can use the jaguar babel command. The syntax of the command is:

jaguar babel [-v] -iinput-format input-file [-h|-d] [range] -ooutput-format [output-file] [-split] 

The -i and -o arguments are required to set the input and output formats, respectively. These are the standard file extensions for the file type, as defined in the List of Extensions. The file formats supported are listed on the Formats page. You can also get a list of formats with the following command (prefixed with $SCHRODINGER/utilities/ on Linux or Mac):

babel -L formats 

Note that the format keywords are not used for the file extensions, as they are when you use the babel and babelg keywords in a Jaguar input file. The input and output file names given in the jaguar babel command are used as they are. This allows for the possibility of a nonstandard extension for the input or output file. If you omit the output file name, or if you give CON as the output file name, the output is written to standard output.

You can add hydrogen atoms to a structure when you do a conversion using the -h option, and you can delete hydrogen atoms from a structure, using the -d option.

Babel can convert multi-structure files to other multi-structure files or to a set of single structure files. You must supply both an input file name and an output file name if you are converting a multi-structure file.

You can select the structures to convert by specifying the range input argument. A valid ranges is in the form "number1-number2", or the word all to select all structures. The quotes are required. For Jaguar output files, the last structure is converted if no range is given; otherwise, the first structure is converted by default.

To generate a set of single structure files, use the -split keyword. The names of these files have a four-digit index number inserted before the file extension. For example, to write individual Jaguar input files (Cartesian) for the 5th through 10th intermediate structures in a Jaguar geometry optimization run, type the command

jaguar babel -ijagout job.out "5-10" -ojagc iter.in -split

The files iter0001.in, iter0002.in, ... iter0006.in are written by Babel.

Babel cannot read Maestro-formatted files. For conversions between Schrödinger file formats that are not recognized by Babel, there is a file conversion utility, jagconvert. This utility reads and writes Jaguar input (.in) and output (.out) files and Maestro (.mae) files. The utility is located in $SCHRODINGER/utilities. The command syntax is as follows:

jagconvert [intype] infileouttypeoutfile

where intype is one of -ijag, -ijin, -ijout, -imae, or -imultimae, and outtype is one of -ojin, -omae, or -omultimae. The input file is assumed to be a Jaguar input file if no input type is explicitly given. MacroModel files are read in using ‑imae. If you convert a file that contains multiple structures, only the first structure in the file is converted to the new format.