FragIt Configuration File Example

FragIt Configuration File Example

FragIt can be used through the command line but it is often more useful to have configuration files. We start out by creating a configuration file which we will call config.ini. In a terminal type

fragit-conf -o config.ini

The default configuration file typically looks like this:

[mergepatterns]
glycine =

[fragmentation]
chargemodel = MMFF94
combinefragments =
writer = GAMESS-FMO
groupcount = 1
maxfragsize = 50

[explicitfragmentpairs]
pairs =

[mfcc]
order = 0

[fragmentpatterns]
a-d-pyranose = [$(C1C(CO)OC(O)C(O)C1(O))][$(OC1C(O)C(O)CC(CO)O1)]
peptide = [$(CN)][$(C(=O)NCC(=O))]
dnabackbone = [$(CCOP)][$(CC1OCCC1)]

[qmmm]
includecovalent = False
includeallwithin = 0.0
hbonddistancemin = 2.5
hbondangle = 110.0
hbonddistancemax = 3.9
includehbondacceptors = False
includehbonddonors = False

[protectpatterns]
nterminal = [$([NH2]),$([NH3])]CC(=O)[$(NCC=O)]

[explicitprotectatoms]
atomids =

[output]
freezebackbone = False
verbose = True
useatomnames = True
buffer = 0.0
writejmol = False
boundaries =
writepymol = False
centralfragment = 0
active = 0.0

We see different configuration groups such as [fragmentation] or [output]. Each group in the configuration file pertains to a different part of FragIt. For instance, the [output] group controls how output files are generated with additional options for more customized output files.

For instance, for complicated structures it is always good to see how the fragmentation looks. FragIt has the ability to generate a PyMol script to help visualize this information.

In the [output] section, change the option writepymol from False to True. When you have corrected your settings you can run FragIt on the command line like

fragit --use-config=config.ini structure.pdb

To see the generated fragmentation you can launch PyMol with the newly generated PyMol script as

pymol structure.inp.pymol

Do note that the PyMol script always has the file ending .pymol and it starts with the base name of your input file.

Other default options?

The fragit-conf tool provides additional configuration options by default which are optimized for different programs / interfaces. The default is FMO for use in the Fragment Molecular Orbital method. To use a specific format you can use the -f option followed by a format code. Currently only BARE, FMO and PE are supported. They are

• BARE: clean sheet configuration file. Will only fragment solute solvent systems.
• FMO: patterns optimized for use in FMO.
• PE: patterns optimized to be used in polarizable embedding potential calculations.