Explicitly cut bonds

So you want to manually specify a place to cut in a structure? This is possible from the configuration file, so here we assume that you've read the basic workflow and have a configuration file.

In the configuration file, there is a section called explicitfragmentpairs and a variable called pairs. By specifying a semi-colon (";") delimited list of pairs (delimited by commas) of atom id's, FragIt will automatically also fragment these points.

Here is an example of what this might look like

[explicitfragmentpairs]
pairs = 2,3;22,23

which would generate two additional fragmentation points. The first between atom 2 and 3 and the second one between atom 22 and 23.