How do I use FragIt?
Once FragIt is installed correctly, you can use it directly from the command line. To see the available options available to you, just run the following
fragit -h
Here we will present the preferred workflow when using FragIt. First, we use FragIt to generate a configuration file which we will modify to our needs. The default way to do this changed in version 1.6.0.
In version 1.6 and later you simply run
fragit-conf -o myconfig.ini
to generate the file myconfig.ini which you can edit in your favourite text editor.
If you use a version prior to this look towards the bottom of this document on how to generate the config file.
It is always nice to be able to visualize the fragmentation to see if anything has gone wrong.
To do this, FragIt can automatically generate appropriate pymol scripts for you to use.
Change the writepymol setting in the [output] section of the myconfig.ini file to True.
Next, get your favorite protonated PDB file (or use the following example file called ala_phe_ala.pdb) to fragment it using FragIt to create an input file (.inp) for the Fragment Molecular Orbital (FMO) method and a .pymol file that we can visualize. Here shown for the example file ala_phe_ala.pdb that is provided.
fragit --use-config=myconfig.ini ala_phe_ala.pdb
Upon completion, the two files are placed in the same directory as the .pdb file.
You can visualize the result by invoking pymol from the command line as
pymol ala_phe_ala.inp.pymol
If you are satisfied with the result, you can run the calculation in GAMESS.
FragIt contains many possibilities to customize the fragmentation procedure. Here are some of the most common options
- Specify new patterns of fragmentation.
- Explicitly define an exact location in a protein to cut.
- Specify a broken bond as protected to avoid cutting that bond.
- Combine several fragments into one.
It was decided to make a separate tool to generate input defaults for different methods in the 1.6.0 release. Prior to that, to generate an input file one would run
fragit --make-config=myconfig.ini
and follow the tutorial as before.