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Format

The Gabedit Format

[Gabedit Format]     (Sphe | Cart)

The workings are with Spherical or Cartezian gaussian Basis format, indicated by the Sphe or Cart keyword.

Coordinates of Atoms for the Electron Density/Molecular orbitals:

[Atoms] (Angs|AU)
element_name number atomic_number x y z
...
The workings are with Angstroms or Atomic Units, indicated by the Angs or AU keyword.

Specification of the basis-set consisting of contracted Gaussian Type Orbitals.

[Basis]
atom_sequence_number1 0
shell_label number_of_primitives 1.00
exponent_primitive_1 contraction_coefficient_1 (contraction_coefficient_1)
...
empty line
atom_sequence__number2 0
shell_label number_of_primitives 1.00
exponent_primitive_1 contraction_coefficient_1 (contraction_coefficient_1)
...
empty line
recognized shell_labels:

's','p','d','f','g','h','i','j','k','sp', 'sd', ....

For 'sp', 'sd'... shells two contraction coefficients must be given, for both first and second functions.

All workings with the [Basis] keyword are in Atomic Units.
 

Specification of the molecular orbitals.

The molecular orbitals and their occupation number are specified in the [MO] section. From this information a density matrix can be constructed.
[MO]
 Sym= symmetry_label_1
 Ene= mo_energy_1
 Spin= (Alpha|Beta)
 Occup= mo_occupation_number_1
 ao_number_1 mo_coefficient_1
 ...
 ao_number_n mo_coefficient_n
 ....
 Sym= symmetry_label_N
 Ene= mo_energy_N
 Spin= (Alpha|Beta)
 Occup= mo_occupation_number_N
 ao_number_1 mo_coefficient_1
 ...
 ao_number_n mo_coefficient_n

Specification of the atomic orbitals.

The atomic orbitals and their occupation number are specified in the [AO] section.
[AO]
Atom= Atomic Symbol_1
Sym= symmetry_label_1
Ene= ao_energy_1
Spin= (Alpha|Beta)
Occup= ao_occupation_number_1
 ao_number_1 ao_coefficient_1
 ...
 ao_number_n ao_coefficient_n
 ....
Atom= Atomic Symbol_i
 Sym= symmetry_label_N
 Ene= ao_energy_N
 Spin= (Alpha|Beta)
 Occup= ao_occupation_number_N
 ao_number_1 ao_coefficient_1
 ...
 ao_number_n ao_coefficient_n
 

Specification of frequencies and corresponding normal coordinates.

The atomic coordinates x,y,z and atomic displacements dx,dy,dz are all in Bohr (Atomic Unit of length).

[FREQ]
 frequency_1
 ...
 frequency_n
  [FR-COORD]
  atom_1_element_string x y z
  ...
 atom_n_element_string x y z
  [FR-NORM-COORD]
 vibration vibration_number_1
 atom_1_dx atom_1_dy atom_1_dz
 ...
 atom_n_dx atom_n_dy atom_n_dz
 ....
 vibration vibration_number_N
 atom_1_dx atom_1_dy atom_1_dz
 ...
 atom_n_dx atom_n_dy atom_n_dz
  [INT]
 ir_intensity_1 raman_intensity_1
 ...
 ir_intensity_n raman_intensity_n
 

The Geometry Convergence section

 The max-force, rms-force, max-step and rms-step sections are optional.
  The atomic coordinates x,y,z are in angstroms unit.

[GEOCONV]
 energy
 geometry1_energy
 ...
 geometryn_energy
 max-force
 geometry_1_maximum_force
 ...
 geometry_n_maximum_force
 rms-force
 geometry_1_rms_force
 ...
 geometry_n_rms_force
 max-step
 geometry_1_maximum_step
 ...
 geometry_n_maximum_step
 rms-step
 geometry_1_rms_step
 ...
 geometry_n_rms_step

  [GEOMETRIES]
 Number_of_atoms
 title or empty line (Geometry number 1)
 atom_1_element_string x y z
 ...
 atom_(Number_of_atoms)_element_string x y z
 ...
 ...
 ...
 Number_of_atoms
 title or empty line (Geometry number n)
 atom_1_element_string x y z
 ...
 atom_(Number_of_atoms)_element_string x y z

Multiple Geometries section

[GEOMS]
numberOfGeometries numberOfLabels
nameLabel1 UnitLabel1 nValue1     /* Example : (Dipole D 3) or (Energy eV 1)*/
nameLabel2 UnitLabel2 nValue2     /* (Dipole D 3) or (Energy eV 1)*/
.....
.....
Value1_1 Value1_2 ....   /* begin geometry number 1 */
Value2_1 Value2_2 ....   /* nValue2 values */
....
....
numberOfAtomsBygeometry1
Symbol1 MMType1 PDBType1 ResiduName1 ResidueNumber1 Charge1 Layer1 X1 Y1 Z1 VX1 VY1 VZ1 /* Ang, Layer = 0, 1, or 2 (HIGHT MEDIUM LOWER), VX1 VY1 VZ1 are optionals */
Symbol2 MMType2 PDBType2 ResiduName2 ResidueNumber2 Charge2 Layer2 X2 Y2 Z2 VX2 VY2 VZ2
....
....
....
Value1 ....   /* begin geometry number 2 */
Value2 ....
....
....
numberOfAtomsBygeometry1
Symbol1 MMType1 PDBType1 ResiduName1 ResidueNumber1 Charge1 Layer1 X1 Y1 Z1 VX1 VY1 VZ1 /* ResiduNumber = 1,2, ...., X, Y and Z in Ang, Layer = 0, 1, or 2 (HIGHT MEDIUM
LOWER)
Symbol2 MMType2 PDBType2 ResiduName2 ResidueNumber2 Charge2 Layer2 X2 Y2 Z2 VX2 VY2 VZ2
....
....
....
......
......

Molecular Dynamics section

[MD]
numberOfGeometries
nAtoms time(fs) TotalEnery(Kcal/mol) Kinetic Potential /* begin geometry number 1 */
Symbol1 X1 Y1 Z1 VX1 VY1 VZ1 Charge1 mmType1 pdbType1 residueName1 residueNumber1 /*Coord in Ang, Velocity in AKMA */
Symbol2 X2 Y2 Z2 VX2 VY2 VZ2 Charge2 mmType2 pdbType2 residueName2
.....
.....
nAtoms time(fs) TotalEnery(Kcal/mol) Kinetic Potential /* begin geometry number 2 */
Symbol1 X1 Y1 Z1 VX1 VY1 VZ1 Charge1 mmType1 pdbType1 residueName1 residueNumber1 /*Coord in Ang, Velocity in AKMA */
Symbol2 X2 Y2 Z2 VX2 VY2 VZ2 Charge2 mmType2 pdbType2 residueName2
.....
.....


Exemple1 :  exampleCartezian.gab

Exemple2 :  exampleSpheric.gab

Exemple3 :  exampleGeoConv.gab