Fragpdb is a python script to create a pdb file where each molecule present in the system is a fragment.
Fragpdb creates the molecular fragments in three steps:

  1. all the possible distances between all the atoms in the system are calculated;
  2. fragpdb calculates the bond lengths using covalent radii for each couple of atoms. The atomic covalent radius is determined by the atomic symbol in the pdb file, and NOT by the atomic name (3rd column in pdb file). In order to have the two atoms bonded, their distance must be shorter than the sum of the two atomic covalent radius, augmented by the bond tolerance (by default 15%);
  3. All the data are sorted by the fragment number, and the new pdb file is written out.

Turning on the verbose mode (-v or —verbose) will force fragpdb to be loud and quite annoying. But it allows to know the number of fragment founded and, if this number does not sound good to you, fragpdb.log log file can be created. In the log file all the distances shorter than 2.5 angstrom are written, as well as the fragment in which each atom is. Please note the run fragpdb in verbose mode can take a loooooooooong (especially with big systems): don't hold your breath, but have a cup of coffee instead.


fragpdb requires python and python-numpy installed


To run fragpdb simply type:

fragpdb [options] -o OUTPUT infile.pdb

The available options are:


show program's version number and exit.

-h, —help

show this help message and exit.

-c, —credits

display credits.

-v, —verbose

be loud and annoying

-o OUTPUT, —output=OUTPUT

output file. This is mandatory


periodic system: atoms are fold back in the unit cell before calculate their connectivity


define cell parameter for periodic systems: a b c (ang) alpha beta gamma (degrees)


Set bond tolerance in % [default: 15.0%]. To check if two atoms are bonded together or not, their distance is compared with the ideal bond length defined as sum of the two atomic covalent radii. This parameter set a tolerance in % on the bond length.


You are free to use, modify and redistribute fragpdb as far as you keep them free as in beer.
As free(as in beer)ware software, fragpdb comes with _ABSOLUTE_ _NO_ (as in NOTHING, NADA, NICTHS, NIENTE, RIEN) WARRANTY. The author is _NOT_ responsible if those software will erase your hard disks, empty your bank account, stole your car, seduce your wife, shave your dog or make any kind of mess and damages, including loss of data or worst. By using polybuild and its libraries, you _ACCEPT_ these terms.


You can download fragpdb here

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