AutoTS: Perform Calculations Panel
Set up and run a transition state search. The setup involves providing a set of reactant and product structures, viewing the reactant and product complexes and an initial reaction path, adjusting these structures as necessary, then making settings and running the job.
To open this panel: click the Tasks button and browse to Quantum Mechanics → AutoTS.
- Using
- Features
- Additional Resources
- Examples
Using the AutoTS: Perform Calculations Panel
The purpose of the AutoTS facility is to find a transition state that leads to a chemical change (rather than just a conformational change, which it attempts to eliminate). The transition state search is done by interpolating between reactants and products to find a guessed transition state. This guess is used in a search and, if successful, the nearest minima on both sides of the reaction are found, by using an intrinsic reaction coordinate (IRC) calculation, and compared to the input. This is done to verify that this transition state is in fact the one that connects the input structures. If the TS does not connect the input structures, additional connections between the reactants and products are searched for. If the TS search fails, the guess is improved in an attempt to converge the calculation. Finally a table is printed that summarizes the results. You can load the results in the AutoTS: View Results Panel by clicking the 
button for the entry. The output file is in the jobname/jobname_AutoTS subdirectory of the working directory, and is named jobname_full_path.mae.
Successful transition state searches depend critically on the quality of the input complexes and the initial guess at the transition state. If these are poor, you can try to manually improve the structures to increase the likelihood of success. A complex path or one in which there is considerable movement of peripheral structures is likely to produce problems in the search.
While AutoTS has the ability to search for multiple transition states that connect input reactants to products (i.e. multi-step reactions) the success rate is likely to be highest for simple, single-step reactions. The suggested strategy for using this tool for a multi-step reaction is to form a hypothesis for the mechanism of your reaction and then treat each step as a separate reaction.
Multiple reactions can be created, either by duplicating a reaction that is already in the panel and editing its structures, or by importing reactant and product structures. When the job is run, a subjob is created for each reaction. The subjobs can be distributed over multiple processors so that they run concurrently.
To write out the input file and a script for running the job from the command line, click the arrow next to the Settings button 
and choose Write.
AutoTS: Perform Calculations Panel Features
- Reaction naming, selection and storage controls
- Set Up Reaction tab
- Preview Reaction Complex tab
- Advanced Settings tab
- Reaction Options section
- Total spin multiplicity of reaction box
- Optimize input molecules option
- Use templates option
- Calculate energies at infinite separation option
- Use intrinsic reaction coordinate (IRC) option and menu
- Apply fallback method if calculation fails option
- Jaguar keywords option and text box
- Special options option text box
- Level of Theory section
- Solvation section
- Conformational Sampling section
- Reaction Options section
- Job toolbar
- Status bar
Reaction naming, selection and storage controls
These controls allow you to name a reaction and save it or export it, and select a reaction to work with.
- Reaction name text box
-
Provide a name for the reaction. The name is used on the reaction option menu, and to label the temporary entry group in the project that stores the structures.
- Duplicate button
-
Duplicate the current reaction. The reaction is given a new default name, which is added to the option menu, and the structures for the original reaction are saved to the current working directory. This feature allows you to take a base reaction and easily make variations on it.
- Export button
-
Export the current reaction to an AutoTS input file. This allows you to subsequently load the reaction using the reaction option menu.
- New button
-
Create a new, empty reaction. The reaction is given a default name, which is added to the option menu.
- Reaction option menu
-
Select the reaction that you want to work with. The choices are the saved reactions, the current (unsaved) reaction, or From file, which opens a file selector, so you can navigate to and choose an AutoTS input file. The reaction data is loaded from this file into the Project Table and the panel.
Set Up Reaction tab
In this tab you set up the reactants and the products for a reaction.
- Reactants section
- Products section
-
Set up the reactants and the products. The same tools are available for reactants and products.
Each reactant or product must be a single molecule. The main part of the section displays the 2D structure of each molecule in a table cell. At the top of the cell are a check box, which controls the inclusion of the structure in the Workspace (linked to the In column in the Entry List or Project Table), and Edit Structure(pencil icon) and Delete structure (X icon) buttons. The Edit Structure button opens the 2D Sketcher panel so you can edit the structure. The Delete Structure button deletes the molecule, which removes it from the panel and deletes its entry from the reaction entry group in the Project Table.
- Sketch button
-
Click this button to sketch a reactant structure in the 2D Sketcher panel. When you have finished sketching the molecule, click Save to add it to the table. A 3D structure is generated from the 2D structure and added to the reaction entry group in the Project Table. You can also double-click in a blank part of the display area (not in a table cell) to open the 2D Sketcher panel.
You can set the charge and spin multiplicity for the molecule in this panel. If any of the atoms in the molecule have a formal charge, you cannot set the molecular charge, as it is determined from the sum of atomic charges. If there are no formal charges, you can set the overall charge on the molecule. If you set the spin multiplicity, you should make sure it is consistent with the number of electrons in the molecule. Note that the overall spin multiplicity of the reaction is set independently, in the Advanced Settings tab.
- Import button
-
Import reactant or product structures. Each structure is split into individual molecules, and each molecule is then used as a reactant or product. Although there are no limits imposed on the number of molecules you can import, all molecules must be active participants in the reaction (not spectators), and reactions with more than 3 reactant or product molecules have not been well tested.
-
From File—Opens a file selector, so you can locate and load the file containing the structures. The file should contain only the reactants or the products.
-
From Project Table (n selected entries)—Use the structures that are selected in the Project Table.
-
From Workspace (n included entries)—Use the structures that are included in the Workspace.
-
From SMILES string—Opens the Import SMILES dialog box so you can enter a SMILES string for the structure. The string is converted into a 3D structure.
-
Preview Reaction Complex tab
Generate reactant and product complexes and a guess at the path, and adjust the structures of the complexes if necessary.
- Generate Complexes button
-
Generate the pre-reactive (entrance) and post-reactive (exit) complexes. These complexes are used to generate a reaction path and transition state guess.
- Generate Reaction Path button
-
Once the complexes are generated, click this button to generate a reaction path.
- Complexes table
-
Lists the reaction complexes and the path, with a check box for including the structure in the Workspace.
- Move Atoms button
-
Use the Workspace tools to adjust the structure of the complex. [Currently not functional; however, as the complexes are just project entries, you can simply include them in the Workspace and adjust them with the usual adjustment tools.]
Advanced Settings tab
Make settings for the reaction complexes, the reaction workflow, and for the individual Jaguar calculations performed in the workflow.
- Reaction Options section
-
Set options for the reaction workflow.
- Total spin multiplicity of reaction box
-
Specify the total spin multiplicity of the reacting system. This value must be provided, as it cannot in general be deduced from the spin multiplicities of the reactants or the products.
- Optimize input molecules option
-
Optimize the structures of the reactant and product molecules separately.
- Use templates option
-
Use stored templates to construct the transition state geometry and reaction path. A template consists of the transition state and the IRC-located endpoints of a successful transition-state search. The input structures are matched to the template structures and the transition state and reaction path are constructed with the help of the template. AutoTS has a default set of templates that can be used. To create your own templates for use in AutoTS, you can use the store_reaction_template Command Help utility.
- Calculate energies at infinite separation option
-
Compute the energies of each reactant and product molecule as isolated molecules. By default, only the energy of the reactant and product complexes are computed. When this option is selected, the energy of reaction is also computed.
- Also compute reaction free energies option
-
Compute the free energies of each reactant and product molecule as isolated molecules. By default, only the energy of the reactant and product complexes are computed. When this option is selected, the free energy of the reaction is also computed. This option involves a frequency calculation on the isolated molecules.
- Use intrinsic reaction coordinate (IRC) option and menu
-
Perform a IRC calculation, and choose the method for calculating the IRC in the option menu:
-
Full—Run a full IRC calculation.
-
Three-Point—Set up an initial point on the IRC path in each direction, and then optimize the geometry for each structure to find the minimum.
-
LQA—use the Local Quadratic Approximation to calculate the IRC.
-
- Apply fallback method if calculation fails option
-
Use artificial force induced reaction (AFIR) method to calculate a path from minima to minima if other methods fail.
- Jaguar keywords option and text box
-
Select the option to specify any extra Jaguar gen section keywords for the calculations, as a comma-separated list of keyword=value settings. For information on these keywords, see The gen Section of the Jaguar Input File
- Special options option and text box
-
Select the option to specify keyword settings for the script that is used to run the transition state search, as a comma-separate list of keyword=value settings.
These tools allow you to specify the default basis set and the default level of theory.
- Theory text box and button
-
Click the button to select the level of theory. A small pane opens with controls for selecting the level of theory. The pane consists of a search text box, a filter button, and a list of available theoretical models. Typing in the text box narrows the list to items that contain the text. Clicking the filter button allows you to set options to restrict the list to certain models, e.g. range-corrected DFT. When you choose an item from the list, the pane closes and the text box (which is noneditable) shows the level of theory you chose.
-
Making a choice of functional sets the dftname keyword in the gen section of the input file.
-
See DFT Keywords in the Jaguar Input File for information on the density functionals.
- Basis set text box and button
-
Click the button to select the basis set. A small pane opens with controls for selecting the basis set. The pane consists of a search text box, a filter button, and a list of basis sets. Typing in the text box narrows the list to basis set names that contain the text. Clicking the filter button allows you to set options to restrict the list to basis sets with certain features: ECP, diffuse functions, pseudospectral, relativistic, RI-MP2 compatible. When you choose a basis set from the list, the pane closes and the text box (which is noneditable) shows the basis set you chose.
See Basis Sets for information on the basis sets available.
- Solvent model option menu
-
Choose the solvent model from this option menu. The default is PCM.
- None—do not include solvation, run a gas phase calculation only.
- PBF—use the standard Poisson-Boltzmann continuum solvation model. This model generally produces better energies than the PCM models.
- PCM—use one of several polarizable continuum models for solvation. The PCM models generally produce smoother convergence in geometry optimizations than the PBF model. See PCM Model for more information on these models. Options for selection of the model (PCM model) and its parameters (PCM radii) are displayed when you choose this option.
- SMD—use the Minnesota solvation model SMD [321]. This model can be used with all available solvents. Available for single-point, geometry optimization, and frequency calculations.
- Solvent text box and button
-
Click the button to select the solvent. A small pane opens with controls for selecting the solvent. The pane consists of a search text box, a filter button, and a list of available solvents. Typing in the text box narrows the list to solvent names that contain the text. Clicking the filter button allows you to set options to restrict the list to solvents with certain features: common, halogenated, aromatic, hydrocarbon, carbonyl, polar, and non-polar solvents. When you choose a solvent from the list, the pane closes and the text box (which is noneditable) shows the solvent you chose. For pKa calculations, the only solvent choices are Water, and DMSO. Water is the default for all except CH and NH acids, whose default is DMSO.
See Solvation Keywords in the Jaguar Input File for a list of available solvents.
Manage job submission and settings. See Job Toolbar for a description of this toolbar.
The Job Settings button opens the AutoTS: Perform Calculations - Job Settings Dialog Box, where you can make settings for running the job.
The status bar displays information about the current job settings and status for the panel. The settings includes the job name, task name and task settings (if any), number of subjobs (if any) and the host name and job incorporation setting. The job status can include messages about job start, job completion and incorporation.
Use the Reset button 
to reset the panel to its default settings and clear any data from the panel.
The status bar also contains the Help button 
, which opens the help topic for the panel in your browser. If the panel is used by one or more tutorials, hovering over the Help button displays a 
button, which you can click to display a list of tutorials (or you can right-click the Help button instead). Choosing a tutorial opens the tutorial topic.
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
{
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
:::
}
}
{
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
:::
}
}
reactant = ['Reaction_1_reactants.mae'] product = ['Reaction_1_products.mae'] multiplicity = 2 &JaguarKeywords basis = 6-31g** dftname = b3lyp-d3 nogas = 2 &
$SCHRODINGER/jaguar run AutoTS.py wflow-autots-0001.in -jobname wflow_autots_0001
Example: Execute the AutoTS.py workflow to find the optimized transition state structure for the Diels-Alder reaction between 1,3-cyclopentadiene and ethylene
{
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
2
reactant_1
0
0
0
1
2
m_atom[11] {
# 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
:::
1 3 0.385284 -1.588966 2.265473 2 6 A0A0A0 0
2 2 1.835016 -1.964944 2.087923 2 6 A0A0A0 1
3 2 2.590904 -0.858052 2.118409 2 6 A0A0A0 2
4 2 1.746210 0.299545 2.310503 2 6 A0A0A0 3
5 2 0.466078 -0.088905 2.399237 2 6 A0A0A0 4
6 41 -0.219688 -1.887994 1.407236 21 1 FFFFFF <>
7 41 -0.048603 -2.052921 3.153430 21 1 FFFFFF <>
8 41 2.171213 -2.986325 1.958515 21 1 FFFFFF <>
9 41 3.668846 -0.833478 2.015118 21 1 FFFFFF <>
10 41 2.095262 1.323016 2.372970 21 1 FFFFFF <>
11 41 -0.402829 0.541231 2.543885 21 1 FFFFFF <>
:::
}
m_bond[11] {
# First column is bond index #
i_m_from
i_m_to
i_m_order
:::
1 1 2 1
2 1 5 1
3 1 6 1
4 1 7 1
5 2 3 2
6 2 8 1
7 3 4 1
8 3 9 1
9 4 5 2
10 4 10 1
11 5 11 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
3
reactant_2
0
0
0
1
2
m_atom[6] {
# 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
:::
1 2 -0.187118 0.627224 -0.208072 2 6 A0A0A0 0
2 2 0.594411 -0.074521 0.625011 2 6 A0A0A0 1
3 41 -0.938121 1.305392 0.170216 21 1 FFFFFF <>
4 41 -0.086370 0.532928 -1.279509 21 1 FFFFFF <>
5 41 1.345414 -0.752690 0.246723 21 1 FFFFFF <>
6 41 0.493663 0.019774 1.696448 21 1 FFFFFF <>
:::
}
m_bond[5] {
# First column is bond index #
i_m_from
i_m_to
i_m_order
:::
1 1 2 2
2 1 3 1
3 1 4 1
4 2 5 1
5 2 6 1
:::
}
}
{
s_m_m2io_version
:::
2.0.0
}
f_m_ct {
s_m_title
i_m_ct_stereo_status
s_st_Chirality_1
s_st_Chirality_2
s_m_entry_id
s_m_entry_name
r_f3d_energy
i_f3d_flags
i_m_Molecular_charge
i_m_Spin_multiplicity
s_sd_enh_stereo_1
i_m_ct_format
:::
product_1
1
2_R_1_7_3_9
5_S_6_7_4_14
4
product_1
0
0
0
1
"M V30 MDLV30/STEABS ATOMS=(2 2 5)"
2
m_atom[17] {
# 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
:::
1 2 4.929232 -5.303818 -2.976691 2 6 A0A0A0 0
2 3 4.147424 -4.731472 -4.155101 2 6 A0A0A0 1
3 3 3.145164 -5.811103 -4.633623 2 6 A0A0A0 2
4 3 4.079857 -6.907657 -5.209762 2 6 A0A0A0 3
5 3 5.487947 -6.304132 -4.981392 2 6 A0A0A0 4
6 2 5.742302 -6.257687 -3.477864 2 6 A0A0A0 5
7 3 5.241056 -4.820568 -5.208428 2 6 A0A0A0 6
8 41 4.800592 -4.995678 -1.946875 21 1 FFFFFF <>
9 41 3.736074 -3.729821 -4.012038 21 1 FFFFFF <>
10 41 2.515594 -6.180715 -3.821793 21 1 FFFFFF <>
11 41 2.485329 -5.415594 -5.408187 21 1 FFFFFF <>
12 41 3.955579 -7.870060 -4.709392 21 1 FFFFFF <>
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15 41 6.429920 -6.907156 -2.951184 21 1 FFFFFF <>
16 41 4.889282 -4.590376 -6.217243 21 1 FFFFFF <>
17 41 6.109778 -4.186345 -5.006170 21 1 FFFFFF <>
:::
}
m_bond[18] {
# First column is bond index #
i_m_from
i_m_to
i_m_order
:::
1 1 2 1
2 1 6 2
3 1 8 1
4 2 3 1
5 2 7 1
6 2 9 1
7 3 4 1
8 3 10 1
9 3 11 1
10 4 5 1
11 4 12 1
12 4 13 1
13 5 6 1
14 5 7 1
15 5 14 1
16 6 15 1
17 7 16 1
18 7 17 1
:::
}
}
reactant = ['Reaction_1_reactants.mae'] product = ['Reaction_1_products.mae'] irc_type = skip_irc &JaguarKeywords basis = 6-31g** dftname = b3lyp-d3 nogas = 2 &
$SCHRODINGER/jaguar run AutoTS.py wflow-autots-0002.in -jobname wflow_autots_0002
Example: Execute the RankReactivity.py workflow script to rank structures by increasing barrier height for a (default) Thiol-Michael Addition reaction with methanethiolate
{
s_m_m2io_version
:::
2.0.0
}
f_m_ct {
s_m_title
b_m_subgroup_collapsed
i_m_Source_File_Index
s_m_Source_File
s_m_Source_Path
s_m_entry_id
s_m_entry_name
s_m_subgroup_title
s_m_subgroupid
i_m_ct_format
:::
methylvinylketone
0
1
wflow-rank_reactivity-0001_acceptors.mae
/Users/furness/Tickets/JAGUAR-13046-STU-ATS-conf/2nd_new/stu_35382
153
methylvinylketone
wflow-rank_reactivity-0001_acceptors
wflow-rank_reactivity-0001_acceptors
2
m_atom[11] {
# 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
i_m_representation
s_m_color_rgb
s_m_atom_name
i_rdk_index
:::
1 2 -0.692120 1.148143 0.000000 2 6 3 A0A0A0 C1 0
2 2 0.000000 0.000000 0.000000 2 6 3 A0A0A0 C2 1
3 2 1.500000 0.000000 0.000000 2 6 3 A0A0A0 C3 2
4 3 2.165112 -1.388966 0.000001 2 6 3 A0A0A0 C4 3
5 15 2.155018 1.039900 -0.000000 70 8 3 FF2F2F O5 4
6 41 -1.772406 1.148142 0.000001 21 1 3 FFFFFF H6 <>
7 41 -0.187696 2.103431 -0.000000 21 1 3 FFFFFF H7 <>
8 41 -0.504423 -0.955289 0.000001 21 1 3 FFFFFF H8 <>
9 41 3.258909 -1.272312 0.000001 21 1 3 FFFFFF H9 <>
10 41 1.858566 -1.938313 -0.890138 21 1 3 FFFFFF H10 <>
11 41 1.858566 -1.938312 0.890141 21 1 3 FFFFFF H11 <>
:::
}
m_bond[10] {
# First column is bond index #
i_m_from
i_m_to
i_m_order
i_m_from_rep
i_m_to_rep
:::
1 1 2 2 3 3
2 1 6 1 3 3
3 1 7 1 3 3
4 2 3 1 3 3
5 2 8 1 3 3
6 3 4 1 3 3
7 3 5 2 3 3
8 4 9 1 3 3
9 4 10 1 3 3
10 4 11 1 3 3
:::
}
}
f_m_ct {
s_m_title
b_m_subgroup_collapsed
i_m_Source_File_Index
s_m_Source_File
s_m_Source_Path
s_m_entry_id
s_m_entry_name
s_m_subgroup_title
s_m_subgroupid
i_m_ct_format
:::
methylacrylate
0
2
wflow-rank_reactivity-0001_acceptors.mae
/Users/furness/Tickets/JAGUAR-13046-STU-ATS-conf/2nd_new/stu_35382
154
methylacrylate
wflow-rank_reactivity-0001_acceptors
wflow-rank_reactivity-0001_acceptors
2
m_atom[12] {
# 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
i_m_representation
s_m_color_rgb
s_m_atom_name
i_rdk_index
:::
1 2 -0.692120 1.148143 0.000000 2 6 3 A0A0A0 C1 0
2 2 0.000000 0.000000 0.000000 2 6 3 A0A0A0 C2 1
3 2 1.500000 0.000000 0.000000 2 6 3 A0A0A0 C3 2
4 16 2.089099 -1.230227 0.000001 70 8 3 FF2F2F O4 3
5 15 2.155018 1.039900 -0.000000 70 8 3 FF2F2F O5 4
6 41 -1.772406 1.148142 0.000001 21 1 3 FFFFFF H6 <>
7 41 -0.187696 2.103431 -0.000000 21 1 3 FFFFFF H7 <>
8 41 -0.504423 -0.955289 0.000001 21 1 3 FFFFFF H8 <>
9 3 3.580640 -1.071154 0.000001 2 6 3 A0A0A0 C9 <>
10 41 4.051401 -2.054253 0.000002 21 1 3 FFFFFF H10 <>
11 41 3.887956 -0.521726 -0.889823 21 1 3 FFFFFF H11 <>
12 41 3.887956 -0.521724 0.889823 21 1 3 FFFFFF H12 <>
:::
}
m_bond[11] {
# First column is bond index #
i_m_from
i_m_to
i_m_order
i_m_from_rep
i_m_to_rep
:::
1 1 2 2 3 3
2 1 6 1 3 3
3 1 7 1 3 3
4 2 3 1 3 3
5 2 8 1 3 3
6 3 4 1 3 3
7 3 5 2 3 3
8 4 9 1 3 3
9 9 10 1 3 3
10 9 11 1 3 3
11 9 12 1 3 3
:::
}
}
f_m_ct {
s_m_title
b_m_subgroup_collapsed
i_f3d_flags
i_m_Source_File_Index
r_f3d_energy
s_m_Source_File
s_m_Source_Path
s_m_entry_id
s_m_entry_name
s_m_subgroup_title
s_m_subgroupid
i_m_ct_format
:::
vinylketone
0
0
3
0
wflow-rank_reactivity-0001_acceptors.mae
/Users/furness/Tickets/JAGUAR-13046-STU-ATS-conf/2nd_new/stu_35382
155
entry
wflow-rank_reactivity-0001_acceptors
wflow-rank_reactivity-0001_acceptors
2
m_atom[8] {
# 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
s_m_atom_name
i_rdk_index
:::
1 2 -0.692120 1.148143 0.000000 2 6 A0A0A0 C1 0
2 2 0.000000 0.000000 0.000000 2 6 A0A0A0 C2 1
3 2 1.500000 0.000000 0.000000 2 6 A0A0A0 C3 2
4 15 2.155018 1.039900 -0.000000 70 8 FF2F2F O8 7
5 41 -1.772406 1.148142 0.000001 21 1 FFFFFF H9 <>
6 41 -0.187696 2.103431 -0.000000 21 1 FFFFFF H10 <>
7 41 -0.504423 -0.955289 0.000001 21 1 FFFFFF H11 <>
8 41 2.040000 -0.935307 0.000000 21 1 FFFFFF "" <>
:::
}
m_bond[7] {
# First column is bond index #
i_m_from
i_m_to
i_m_order
:::
1 1 2 2
2 1 5 1
3 1 6 1
4 2 3 1
5 2 7 1
6 3 4 2
7 3 8 1
:::
}
}
{
"reaction_name": "Michael-Addition",
"reaction_type":
["Michael-Addition-Thiolate-Enone",
"Michael-Addition-Thiolate-Ynone",
"Michael-Addition-Thiolate-Ene-Sulfone",
"Michael-Addition-Thiolate-Yne-Sulfone"],
"autots_template": "wflow-rank_reactivity-0001_template.in",
"slope": 1.0,
"intercept": 0.0,
"energy_type": "energy",
"reactivity_metric_name": "barrier height (kcal/mol)"
}
ts_acceptance_strictness = loose optimize_inputs = True conf_search = True free_energy = False &JaguarKeywords basis = 6-31g* dftname = wb97x isolv = 7 nogas = 2 iusediffuse=1 &
$SCHRODINGER/jaguar run RankReactivity.py -jobname wflow-rank_reactivity-0001 -reactant_file wflow-rank_reactivity-0001_acceptors.mae -config_file wflow-rank_reactivity-0001_config.json -subdir
Example: Execute the RankReactivity.py workflow script to rank structures by increasing barrier height for a (user-defined) Williamson Ether synthesis
{
s_m_m2io_version
:::
2.0.0
}
f_m_ct {
s_m_title
s_m_entry_id
s_m_entry_name
i_m_ct_format
:::
methoxide
1
methoxide
2
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
i_m_formal_charge
i_m_representation
s_m_color_rgb
s_m_atom_name
i_rdk_index
:::
1 3 0.179314 0.308946 0.227596 2 6 0 3 A0A0A0 C1 0
2 18 -0.471016 -0.771440 -0.332971 70 8 -1 3 FF2F2F O2 1
3 41 1.068732 -0.035952 0.754930 21 1 0 3 FFFFFF H3 <>
4 41 0.470303 1.005739 -0.558473 21 1 0 3 FFFFFF H4 <>
5 41 -0.487424 0.810399 0.929097 21 1 0 3 FFFFFF H5 <>
:::
}
m_bond[4] {
# First column is bond index #
i_m_from
i_m_to
i_m_order
i_m_from_rep
i_m_to_rep
:::
1 1 2 1 3 3
2 1 3 1 3 3
3 1 4 1 3 3
4 1 5 1 3 3
:::
}
}
{
s_m_m2io_version
:::
2.0.0
}
f_m_ct {
s_m_title
s_m_entry_id
s_m_entry_name
i_m_ct_format
:::
chloromethane
1
chloromethane
2
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
i_m_representation
s_m_color_rgb
i_rdk_index
:::
1 3 0.787648 0.872740 0.513368 2 6 3 A0A0A0 0
2 57 1.201805 1.668017 2.052189 9 17 3 006400 1
3 41 -0.289866 0.712536 0.475986 21 1 3 FFFFFF <>
4 41 1.097367 1.514199 -0.311679 21 1 3 FFFFFF <>
5 41 1.308204 -0.083274 0.457165 21 1 3 FFFFFF <>
:::
}
m_bond[4] {
# First column is bond index #
i_m_from
i_m_to
i_m_order
i_m_from_rep
i_m_to_rep
:::
1 1 2 1 3 3
2 1 3 1 3 3
3 1 4 1 3 3
4 1 5 1 3 3
:::
}
}
f_m_ct {
s_m_title
s_m_entry_id
s_m_entry_name
i_m_ct_format
:::
chloroethane
2
chloroethane
2
m_atom[8] {
# 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
i_m_representation
s_m_color_rgb
i_rdk_index
:::
1 3 0.000000 0.000000 0.000000 2 6 3 A0A0A0 0
2 57 -0.579074 1.684231 0.000000 9 17 3 006400 1
3 3 1.500000 0.000000 0.000000 2 6 3 A0A0A0 2
4 41 -0.372154 -0.502719 0.892679 21 1 3 FFFFFF <>
5 41 -0.372155 -0.502720 -0.892677 21 1 3 FFFFFF <>
6 41 1.863333 -1.027662 -0.000000 21 1 3 FFFFFF <>
7 41 1.863333 0.513831 -0.889981 21 1 3 FFFFFF <>
8 41 1.863333 0.513831 0.889981 21 1 3 FFFFFF <>
:::
}
m_bond[7] {
# First column is bond index #
i_m_from
i_m_to
i_m_order
i_m_from_rep
i_m_to_rep
:::
1 1 2 1 3 3
2 1 3 1 3 3
3 1 4 1 3 3
4 1 5 1 3 3
5 3 6 1 3 3
6 3 7 1 3 3
7 3 8 1 3 3
:::
}
}
f_m_ct {
s_m_title
s_m_entry_id
s_m_entry_name
i_m_ct_format
:::
chloropropane
3
chloropropane
2
m_atom[11] {
# 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
i_m_representation
s_m_color_rgb
s_m_atom_name
i_rdk_index
:::
1 3 0.000000 0.000000 0.000000 2 6 3 A0A0A0 C1 0
2 57 -0.579074 1.684231 0.000000 9 17 3 006400 Cl2 1
3 3 1.500000 0.000000 0.000000 2 6 3 A0A0A0 C3 2
4 3 -0.512139 -0.691816 1.228456 2 6 3 A0A0A0 C4 3
5 41 -0.372154 -0.502718 -0.892678 21 1 3 FFFFFF H5 <>
6 41 1.863333 -1.027662 -0.000000 21 1 3 FFFFFF H6 <>
7 41 1.863333 0.513831 -0.889981 21 1 3 FFFFFF H7 <>
8 41 1.863333 0.513831 0.889981 21 1 3 FFFFFF H8 <>
9 41 -0.162222 -1.724090 1.236647 21 1 3 FFFFFF H9 <>
10 41 -0.144306 -0.176438 2.115690 21 1 3 FFFFFF H10 <>
11 41 -1.602043 -0.677638 1.225709 21 1 3 FFFFFF H11 <>
:::
}
m_bond[10] {
# First column is bond index #
i_m_from
i_m_to
i_m_order
i_m_from_rep
i_m_to_rep
:::
1 1 2 1 3 3
2 1 3 1 3 3
3 1 4 1 3 3
4 1 5 1 3 3
5 3 6 1 3 3
6 3 7 1 3 3
7 3 8 1 3 3
8 4 9 1 3 3
9 4 10 1 3 3
10 4 11 1 3 3
:::
}
}
{
"reaction_name": "Williamson Ether synthesis",
"reaction_type": "Williamson Ether synthesis",
"autots_template": "wflow-rank_reactivity-0002_template.in",
"slope": 1.0,
"intercept": 0.0,
"energy_type": "energy",
"reactivity_metric_name": "barrier height (kcal/mol)"
}
[
{
"reaction_name": "Williamson Ether synthesis",
"reaction_steps": [
{
"reaction_smarts": "[F,Cl,Br,I:1][C@:2].[C:4][O-1:3]>>[C:4][OH0+0:3][C@@:2].[X-:1]",
"reactant_smiles": [
"CF",
"C[O-]"
]
}
]
}
]
ts_acceptance_strictness = loose optimize_inputs = True conf_search = True free_energy = False &JaguarKeywords basis = 6-31g* dftname = wb97x isolv = 7 nogas = 2 iusediffuse=1 &
$SCHRODINGER/jaguar run RankReactivity.py -jobname wflow-rank_reactivity-0002 -reactant_file wflow-rank_reactivity-0002_substrates.mae wflow-rank_reactivity-0002_nucleophiles.mae -reaction_file wflow-rank_reactivity-0002_reaction.json -config_file wflow-rank_reactivity-0002_config.json -subdir