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FragIt is a python based tool that allows you to quickly fragment "any" molecule and use the produced output file(s) as an a starting point for input files in quantum chemistry programs that supports such fragment based methods.

FragIt was made out of the need to quickly benchmark many different molecules while developing new fragment based methods and is now being released in the hope that it is useful for others in their research. You can read about FragIt in the published paper.

Currently, FragIt supports the fragment molecular orbital method in GAMESS. FragIt also comes with a standard purpose XYZ writer that dumps each fragment in a separate .xyz file. Finally, there is a new XYZ-MFCC writer to support molecular fragmentation with conjugate caps that will yield capped fragments and caps for MFCC. New output writers can be added easily to support other methods and programs.

Obtaining FragIt

Since you found this file, it is obvious that you also found the source code. You can obtain the latest version from github where tagged releases are also available.

Installing FragIt

FragIt is a python library and installation is quite straight forward

python install

to install it in the default locations. To install it in a custom location, you can run the following

python install --prefix=/path/to/custom/installation

Remember to add the installation paths to your environment variables:

export PATH=/path/to/custom/installation/bin:$PATH
export PYTHONPATH=/path/to/custom/installation/lib/python2.7/site-packages:$PYTHONPATH

shown here for a python 2.7 installation example.

Running FragIt

in a terminal, you can type


to see its help message.

See the wiki for more examples of how to use FragIt.


In order to run FragIt, you need the following installed on your system: