Molecular geometry

Basics

In the input, the geometry is specified by the geometry keyword. Multiple options are available:

• Read the geometry from external file - the geometry keyword is set to a name of a file containing the geometry. Cuby can read multiple standard file formats incuding common .xyz and PDB files. The format of the file is determined automatically either from the filename suffix or from its contents. For example:

  geometry: my_geometry_file.xyz

• Enter the geometry inline in the YAML input - the geometry can be entered directly in the input file as a multi-line YAML string where each line contains the element and xyz coordinates:

  geometry: |
    O   -0.000000000   0.000000000   0.017677310
    H    0.000000000   0.755896950  -0.527614050
    H   -0.000000000  -0.755896950  -0.527614050

• Read the geometry from Cuby's database - Cuby contains a database of frequently used structures and it is possible to define new databases as well. The syntax is database_name:structure_name, e.g. for water dimer from the S66 data set:

  geometry: S66:water_dimer

• Build the geometry from SMILES string - the geometry can be built from a SMILES string using syntax:

  geometry: SMILES:c1ccccc1 # this is benzene

Specify geometry from commandline

Note that the value of the geometry keyword can be set from the commandline using a -g shortcut. It is therefore possible to run cuby calculation on any geometry file by typing e.g.

cuby4 input.yaml -g geometry_file.xyz

File formats

Cuby supports following file formats:

File format	Filename	Read	Write	Comments
XYZ	*.xyz	yes	yes	with extensions described elsewhere in the documentation
	*.pdb	yes	yes	modified version with more precise coordinates an be used as *.lpdb
Tripos MOL2	*.mol2	yes	yes
SDF	*.sdf	yes	no
Z-matrix	*.zmat, *.gzmat	yes	no	format compatible with Gaussian, converted to cartesian upon reading
Turbomole	*.coord	yes	yes	cartesian coordinates in in atomic units

Geometry databases

The geometry databases can be found in directory cuby4/data/geometries. Each database consists of a tarball containing the geometry files and a YAML file that assings names to the filenames.

The geometry datbases are often associated with data sets of benchmark data; for each of the data sets listed, there's a database of geometries of the same name.

SMILES

The molecular geometry can be built from the SMILES notation.

Cuby uses an external tool for this, the Balloon program. To use this feature, a path to Balloon has ta be configured using keyword balloon_dir.

Modifications

Upon loading the geometry, it can be modified by following keywors (in this order):

1. geometry_update_coordinates - The coordinates in the geometry are updated with coordinates from another file. This is useful for e.g. loading modified coordinates from an .xyz file into geometry in PDB format containing additional information.
2. geometry_rotate - The geometry is rotated around its origin in x,y,z axes.
3. geometry_reorder - Change the order of the atoms.
4. ghost_atoms - Selected atoms can be labaled as "ghost atoms" posessing basis set but no charge in QM calculations.
5. selection - cut only selected atoms from the geometry.

More options of modifying a geometry are provided by the geometry protocol

Multiple geometries in file

Some protocols such as the protocol scan read multiple geometries from one file. In such case, .xyz format with multiple entries is used.

Additional data in geometry files

To simplify mass processing of different molecules using a single input file, Cuby can read the charge and multiplicity of the system from the geometry file. This feature has to be enabled in the input using the keyword geometry_setup_from_file. When one or both values are ommited, charge 0 and multiplicity 1 are assumed.

In a .xyz file, the data should be present at the second line of the file in format 'charge=X multiplicity=Y'. There is an example for hydrogen molecule anion:

2
charge=-1 multiplicity=2
H 0.000 0.000 0.000
H 0.000 0.000 0.600 

In PDB files, charge and multiplicity are read from REMARK statements that can be placed anywhere in the file. An example:

REMARK charge -1
REMARK multiplicity 2

In .mol2 files, the total charge is calculated as a sum of atomic charges. Reading multiplicity is not supported.