AutoTS: View Results Panel

Display a summary of the results of a transition state search, including a diagram of the reaction path, list of structures, and summary of energies.

To open this panel: click the Tasks button and browse to Quantum Mechanics → AutoTS Results. To open the panel for the results of a job and load the results, use the Workflow Action Menu for the results entry in the Entry List (Entries).

Features
Additional Resources
Examples

Load results from option menu

Choose the structure source for viewing the AutTS results.

Project Table (n selected entries)—Use the entries that are currently selected in the Project Table or Entry List. The number of entries selected is shown on the menu item. An icon is displayed to the right which you can click to open the Project Table and select entries. When this option is selected, a Load button is displayed to the right.

Open Project Table button

Open the Project Table panel, so you can select the entries for the structure source.

File name text box and Browse button

Enter the name of the Maestro file containing the transition state results in the text box, or click Browse to navigate to the file. The file is in the jobname subdirectory of the working directory, and is named jobname_full_path.mae.

Calculation summary data

Displays the reaction energy, and enthalpy if it is available.

Structure table

This table lists the stationary point structures found: reactant and product complexes, transition states, and intermediates, with a check box for each structure to display it in the Workspace.

Type of energy property options

Select the energy property to display in the summary and the display area. The options available depend on the options you selected in the Advanced Settings tab of the AutoTS: Perform Calculations Panel.

Complex—Use the energies of the reactant and product complex as the reactant and product energies.
Infinitely separated—Use the energies of the reactants and products at infinite separation (i.e. the individual molecules)
Free (298K)—Use the free energies at 298K of the individual reactant and product molecules, transition states, and intermediates.

Export button

Export the results to a file and export the diagram as an image.

Display area

Displays an energy diagram of the reaction. The stages of the reaction are labeled with the name from the structure table and the energy relative to the reactants, calculated for the chosen type of energy property.

Tutorials

Workflow Examples

Example: Execute the AutoTS.py workflow to find the optimized transition state structure for a hydrogen abstraction reaction between ethane and hydrogen atom

Example input structure file (Reaction_1_reactants.mae):

{ 
 s_m_m2io_version
 :::
 2.0.0 
} 

f_m_ct { 
 s_m_title
 i_m_ct_stereo_status
 s_m_entry_id
 s_m_entry_name
 r_f3d_energy
 i_f3d_flags
 i_m_Molecular_charge
 i_m_Spin_multiplicity
 i_m_ct_format
 :::
 reactant_1 
  1
  16 
  reactant_1 
  0
  0
  0
  1
  2
 m_depend[1] { 
  # First column is dependency index #
  i_m_depend_dependency
  s_m_depend_property
  :::
  1 20 i_m_Spin_multiplicity 
  :::
 } 
 m_atom[5] { 
  # First column is atom index #
  i_m_mmod_type
  r_m_x_coord
  r_m_y_coord
  r_m_z_coord
  i_m_color
  i_m_atomic_number
  s_m_color_rgb
  i_rdk_index
  b_rdkit_hasAdvancedQuery
  :::
  1 3 0.000000 0.000000 0.000000 2 6 A0A0A0  0 0
  2 41 -0.363333 1.027662 0.000000 21 1 FFFFFF  <> <>
  3 41 -0.363333 -0.513831 0.889981 21 1 FFFFFF  <> <>
  4 41 -0.363333 -0.513831 -0.889981 21 1 FFFFFF  <> <>
  5 41 1.090000 0.000000 0.000000 21 1 FFFFFF  <> <>
  :::
 } 
 m_bond[4] { 
  # First column is bond index #
  i_m_from
  i_m_to
  i_m_order
  :::
  1 1 2 1
  2 1 3 1
  3 1 4 1
  4 1 5 1
  :::
 } 
} 

f_m_ct { 
 s_m_title
 i_m_ct_stereo_status
 s_m_entry_id
 s_m_entry_name
 r_f3d_energy
 i_f3d_flags
 i_m_Molecular_charge
 i_m_Spin_multiplicity
 i_m_ct_format
 :::
 reactant_2 
  1
  17 
  reactant_2 
  0
  0
  0
  2
  2
 m_depend[1] { 
  # First column is dependency index #
  i_m_depend_dependency
  s_m_depend_property
  :::
  1 20 i_m_Spin_multiplicity 
  :::
 } 
 m_atom[1] { 
  # First column is atom index #
  i_m_mmod_type
  r_m_x_coord
  r_m_y_coord
  r_m_z_coord
  i_m_color
  i_m_atomic_number
  s_m_color_rgb
  i_rdk_index
  b_rdkit_hasAdvancedQuery
  :::
  1 48 0.000000 0.000000 0.000000 21 1 FFFFFF  0 0
  :::
 } 
}

Example input structure file (Reaction_1_products.mae):

{ 
 s_m_m2io_version
 :::
 2.0.0 
} 

f_m_ct { 
 s_m_title
 i_m_ct_stereo_status
 s_m_entry_id
 s_m_entry_name
 r_f3d_energy
 i_f3d_flags
 i_m_Molecular_charge
 i_m_Spin_multiplicity
 i_m_ct_format
 :::
 product_1 
  1
  18 
  product_1 
  0
  0
  0
  2
  2
 m_depend[1] { 
  # First column is dependency index #
  i_m_depend_dependency
  s_m_depend_property
  :::
  1 20 i_m_Spin_multiplicity 
  :::
 } 
 m_atom[4] { 
  # First column is atom index #
  i_m_mmod_type
  r_m_x_coord
  r_m_y_coord
  r_m_z_coord
  i_m_color
  i_m_atomic_number
  s_m_color_rgb
  i_m_unpaired_electrons
  i_rdk_index
  b_rdkit_hasAdvancedQuery
  :::
  1 14 0.000000 0.000000 0.000000 2 6 A0A0A0  1 0 0
  2 41 -0.099194 1.066189 -0.140608 21 1 FFFFFF  <> <> <>
  3 41 -0.603812 -0.679952 -0.582653 21 1 FFFFFF  <> <> <>
  4 41 0.703086 -0.386170 0.723162 21 1 FFFFFF  <> <> <>
  :::
 } 
 m_bond[3] { 
  # First column is bond index #
  i_m_from
  i_m_to
  i_m_order
  :::
  1 1 2 1
  2 1 3 1
  3 1 4 1
  :::
 } 
} 

f_m_ct { 
 s_m_title
 i_m_ct_stereo_status
 s_m_entry_id
 s_m_entry_name
 r_f3d_energy
 i_f3d_flags
 i_m_Molecular_charge
 i_m_Spin_multiplicity
 i_m_ct_format
 :::
 product_2 
  1
  19 
  product_2 
  0
  0
  0
  1
  2
 m_depend[1] { 
  # First column is dependency index #
  i_m_depend_dependency
  s_m_depend_property
  :::
  1 20 i_m_Spin_multiplicity 
  :::
 } 
 m_atom[2] { 
  # First column is atom index #
  i_m_mmod_type
  r_m_x_coord
  r_m_y_coord
  r_m_z_coord
  i_m_color
  i_m_atomic_number
  s_m_color_rgb
  i_rdk_index
  b_rdkit_hasAdvancedQuery
  :::
  1 41 0.025959 0.054673 -0.348787 21 1 FFFFFF  0 0
  2 41 -0.025959 -0.054673 0.348787 21 1 FFFFFF  1 0
  :::
 } 
 m_bond[1] { 
  # First column is bond index #
  i_m_from
  i_m_to
  i_m_order
  :::
  1 1 2 1
  :::
 } 
}

Example input file (wflow-autots-0001.in):

reactant = ['Reaction_1_reactants.mae']
product = ['Reaction_1_products.mae']
multiplicity = 2
&JaguarKeywords
basis = 6-31g**
dftname = b3lyp-d3
nogas = 2
&

To submit the job from the command line, download the input files (below) and enter the following command:

$SCHRODINGER/jaguar run AutoTS.py wflow-autots-0001.in -jobname wflow_autots_0001

Click a button to download the file. The Output files are those produced when the job is run.

Files generated with release version: 2024-4

Input structure: Reaction_1_reactants.mae

Input structure: Reaction_1_products.mae

Input file: wflow-autots-0001.in

Output files

Example: Execute the AutoTS.py workflow to find the optimized transition state structure for the Diels-Alder reaction between 1,3-cyclopentadiene and ethylene

Note: By default, AutoTS runs an IRC calculation after locating the TS. This has been turned off in the .in file for this example.