Interface fragmentation

This interface implements the Kernel Energy Method[1] (KEM) up to second order. The energy of the system is composed from calculation of fragments and all their dimers. Fragments with dangling bonds are capped with hydrogens.

Cuby offers automation of the fragmentation process, non-covalent fragments are recognized automatically and fragmentation across covalent bonds is defined just by a list of bonds to be broken.

This interface can be also used for building fragments for other calculations. Running the interface with the keyword fragmentation_geometry_only set produces files containing all the fragments and their dimers. PDB format is used and each of the fragment or dimer is saved as a separate residue. If the filename has suffix .lpdb instead of .pdb, the coordinates are written with more decimal places. This PDB in 'long format' can be used as input for other Cuby calculations.

  1. Huang, L.; Massa, L.; Karle, J. Int. J. Quantum Chem. 2005, 103 (6), 808–817.

Methods and capabilities

The interface implements a single unnamed method; 'method' keyword not necessary

Input structure

The interface requires following blocks in the input:

Keywords used

Keywords specific for this interface:

Other keywords used by this interface:


The following examples, along with all other files needed to run them, can be found in the directory cuby4/interfaces/fragmentation/examples

# Fragmentation example 1

# Calculation of butane molecule which is built from three fragments -
# CH4, C2H6 and CH4.

# The PM6 calculation of this system yields energy 14.413 kcal/mol
# This fragmented calculation yields               14.436 kcal/mol

job: energy
interface: fragmentation


# The bonds to be cut (two atom selections) and a ratio determining the length of
# the bond to the link atom (C-H) from the length of the original C-C bond.
  - "11; 12; 0.7211"
  - "13; 14; 0.7211"

# If the following lines are uncommented, the fragments and their dimers are built
# and saved but no calculation is run on them:
#prepare_only: yes
#fragmentation_geometry_only: yes

# Method of calculation applied to the fragments is specified in a separate
# block:
  method: pm6
  charge: 0
# Fragmentation example 2 - peptide fragmentation

# The inetrafec can be used just for preparing the geometry of the fragments.
# Here, it is used to fragment a peptide into AA sidechains and individual
# segments of the backbone.

# We setup an energy calculation but the keyword fragmentation_geometry_only
# makes the job skip the actual calculation
job: energy
interface: fragmentation
fragmentation_geometry_only: yes

# Geometry - must be in pdb format. A small polypeptide from internal database
# is used.
geometry: PDB:1AQG

# The bonds to be cut are specified by PDB names of the atoms
# The third entry is the ratio of the original (C-C) and newly added C-H 
# bond length
  # This selects the C-C bonds in the backbone
  - "%atomname(C); %atomname(CA); 0.7211"
  # This selects the C_alpha-C_beta bonds to sidechains. Note that proline
  # is excluded because in that case this bond is part of the ring
  - "%atomname(CB)&:~PRO; %atomname(CA); 0.7211"

# Multiple options for naming the created residues are avilable, here wee keep
# the original names but downcased.
fragmentation_monomer_names: downcase

# The fragments are written into file "fragments.pdb"
# This prevents writing another file with dimers of teh fragments:
fragmentation_dimer_file: ""