Protocol geometry

This protocol processes the input geometry and writes it to a file. No calculation is ran.

In addition to the standard modifications of geometry (listed on the geometry page), additional actions can be called using the geometry_action keyword.

Keywords used

Keywords specific for this protocol:

Other keywords used by this protocol:

Examples

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

#===============================================================================
# Geometry protocol example 1 - standard geometry manipulations
#===============================================================================

# This example shows processing the input geometry using the manipulations that
# can be applied to any geometry loaded into cuby. These are controleld by
# keywords:
# * selection
# * reorder
# * rotate
# * update_coordinates

# Here, the input geometry is loaded from the S66 data set and only the first
# molecule from the dimer is saved in PDB format.

job: geometry
geometry: S66:01 # water_dimer
selection: "1-3"
geometry_write: water1.pdb

#===============================================================================
# Geometry protocol example 2 - actions available in this protocol
#===============================================================================

# This is example of a multi-step job that does the following:
# 1) extracts one molecule from a dimer
# 2) optimizes the extracted molecule
# 3) loads the optimized monomer coordinates back into the dimer

job: multistep
steps: extract, optimize, update

calculation_extract: # Extract the monomer
  job: geometry
  geometry: water_dimer.pdb
  selection: ":1" # First residue
  geometry_write: water1.pdb

calculation_optimize: #  optimization
  job: optimize
  interface: mopac
  method: am1
  charge: 0
  geometry: water1.pdb
  restart_file: optimized.pdb
  optimize_print: [final_energy] # Do not print each step of optimization

calculation_update: # Update the dimer
  job: geometry
  geometry: water_dimer.pdb # Original dimer geometry
  geometry2: optimized.pdb # New geometry of the monomer
  geometry_action: partial_pdb_update
  geometry_write: updated_dimer.pdb

#===============================================================================
# Geometry protocol example 3 - build water dimer using connectors
#===============================================================================

# This is example of a multi-step job that build two water molecules
# with dummy atom connectors and connects them.

job: multistep
steps: mono1, mono2, connect

calculation_mono1: # Build monomer 1 with connector on O
  job: geometry
  geometry: |
    O    0.000000000   0.000000000   0.000000000
    H   -0.583458892  -0.762495884   0.000000000
    H   -0.583837701   0.762495884  -0.000000000
  geometry_action: add_connector
  geometry_write: water_O.xyz
  # Connector on O, perpendicular to molecular plane
  connector_type: perpendicular
  # Selection to the atom to connect to, the other two atoms define the plane:
  connector_orientation: "1; 2; 3"

calculation_mono2: # Build monomer 2 with connector on H
  job: geometry
  geometry: |
    O    0.000000000   0.000000000   0.000000000
    H   -0.583458892  -0.762495884   0.000000000
    H   -0.583837701   0.762495884  -0.000000000
  geometry_action: add_connector
  geometry_write: water_H.xyz
  # Connector on H, in extension of the bond
  connector_type: linear
  # Selection to the atom to connect to, second selection defines the angle
  # and the third one a plane:
  connector_orientation: "2; 1; 3"

calculation_connect:
  job: geometry
  geometry: water_O.xyz
  geometry2: water_H.xyz
  # Connect the connectors
  geometry_action: connect
  # The molecules point to opposite sides from the axis:
  geometry_connect_orientation: max_center_dist
  # In addition, build a scan of geometries bith intermolecular distance
  # scaled by these factors:
  geometry_connect_scan_vdw: [0.8, 0.85, 0.9, 0.95, 1.0, 1.05, 1.1, 1.25, 1.5, 2.0]