Interface h_bonds4

The latest empirical correction for hydrogen bonding (H4) in semiempirical methods.[1] To get the complete D3H4 correction, add also the corresponding D3 dispersion correction. Halogen bonds can be corrected using yet another interface.

Default parameters are available (and automatically assigned) for following semiempirical methods: PM6, AM1, PM3, RM1, OM3 and SCC-DFTB.

  1. Řezáč, J.; Hobza, P. J. Chem. Theory Comput. 2012, 8, 141–151.

Methods and capabilities

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

Keywords used

Keywords specific for this interface:

Examples

The following examples, along with all other files needed to run them, can be found in the directory cuby4/interfaces/h_bonds4/examples

#===============================================================================
# H-bonds4 example 1: Interaction energy calculation with PM6-D3H4
#===============================================================================

# In this example, the D3 and H4 corrections (designed to be used together)
# are added to PM6 in calculation of interaction energy

job: interaction
method: pm6
interface: mopac

# This interface is called as a modifier, its result is added to the underlying
# PM6 calculation performed in MOPAC
modifiers: dispersion3, h_bonds4
# No setup for the modifiers is needed, the default parameters are identified
# and applied automagically.

# Geometry: Water dimer from the S66 data set
geometry: S66:water_dimer
charge: 0

# Print energy components, in this case the contributions of the corrections
print: energy_decomposition

#-------------------------------------------------------------------------------
# Note
#-------------------------------------------------------------------------------
# This calculation prints a warning on selection in non-PDB file. This is
# because the H4 correction contains a special term applied to charged residues
# which can be identified only when the input is a PDB file.