Jaguar Spectroscopy Panel

Circular Dichroism, Dichroism, VCD, ECD, NMR, UV, IR, jaguar spectroscopy, chemical shift

Calculate VCD, ECD, or NMR spectra for a set of structures, with optional MM conformational search and QM refinement.

To open this panel, click the Tasks button and browse to Quantum Mechanics → Spectroscopy Workflows.

  • Using
  • Features
  • Additional Resources
  • Examples

Using the Jaguar Spectroscopy Panel

This panel performs all the necessary tasks to create VCD, ECD, or NMR spectra that are conformationally averaged. The structural input must be either a single molecule or a set of conformers. If the input structure is a single molecule, it is first processed by MacroModel to generate conformers for each structure. These structures are then optimized by Jaguar, and the results are processed again by MacroModel, this time to eliminate redundant conformers and conformers that are too high in energy. The remaining conformers are then processed by Jaguar to calculate the spectra. Boltzmann weights are added as a property so that the conformational averaging takes into account the thermal population of the conformers. In addition to the spectra for the individual conformers, Boltzmann-averaged spectrum files are written out: a : .spm file for the stick spectrum, (one for each form of the dipole operator for ECD spectra, one for each enantiomer for VCD spectra), and a .csv file for the broadened, normalized spectra. See spectroscopy.py: Calculation of Boltzmann-Averaged Properties for details on the output files and properties.

As the workflow involves running multiple independent Jaguar calculations, you can distribute the subjobs for these calculations over multiple processors, by making settings in the Job Settings Dialog Box.

When the calculation finishes, you can use the Spectrum Plot Panel to display the spectra. If you have experimental data, you can run the spectrum_align Command Help utility to align the predicted and experimental spectra. The utility calculates the correlation coefficient between the predicted and experimental spectra. A positive coefficient means the spectra are for the same enantiomer; a negative coefficient means the spectra are for opposite enantiomers. See spectrum_align: Align Predicted and Experimental Circular Dichroism Spectra for more information.

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. For information on command usage and options, see spectroscopy.py Command Help.

Jaguar Spectroscopy Panel Features

Use structures from option menu

Choose the structure source for the circular dichroism spectra. If multiple structures are specified, they must be conformers of a single molecule.

  • 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.
  • Workspace (included entry)—Use the entry that is currently included in the Workspace. Only one entry must be included in the Workspace.
  • File—Use the specified file. When this option is selected, the File name text box and Browse button are displayed.
Open Project Table button

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

File name text box and Browse button

Enter the file name in this text box, or click Browse and navigate to the file. The name of the file you selected is displayed in the text box.

Calculate spectra option menu

Select the type of spectra to calculate.

  • VCD and IR—Calculate vibrational circular dichroism (VCD) and IR spectra.
  • IR only—Calculate IR spectra.
  • ECD and UV/vis—Calculate electronic circular dichroism (ECD) spectra. These calculations require a TDDFT calculation.
  • UV/vis only— Calculate UV/Visible spectra. These calculations require a TDDFT calculation.
  • NMR—Calculate NMR chemical shifts, NMR spin-spin couplings between atom pairs, and Nuclear Overhauser Effect (NOE) Boltzmann-averaged distances of H-H and H-F vectors. Use the NMR options link to make additional selections for the NMR calculation. NMR chemical shifts in solvent are only available for 13C and 1H.
NMR options link

Click this link to display a pane of options for NMR calculations. Only available if NMR is selected.

Generate spectra for option menu

Select the nuclei for which spectra should be generated, from 1H, 11B, 13C, 15N, 19F and 31P. If no options are selected, chemical shifts and spin-spin couplings are still computed but no spectra are generated.

Simulate Boltzmann-averaged spectra only option

Skip calculation of individual conformer spectra and compute a Boltzmann-averaged NMR spectrum.

Spectral resolution option menu

Set the resolution of the NMR spectrum, which determines the number of points used in the NMR spectrum simulation. Select Coarse to set the resolution to 0.01 ppm, Medium to set the resolution to 0.02 ppm, and Fine to set the resolution to 0.0005 ppm.

Spectrometer frequency text box

Sets the strength of the NMR magnetic field, in MHz

Coupling constant threshold text box

Set the value in Hz below which J-couplings are omitted from the spectrum simulation, as their effects are below the resolution of most spectrometers. Lowering this value may give additional splitting detail for conjugated systems at the cost of significantly increased runtime and memory use.

Use conformational search option

Perform a conformational search on the input structure with MacroModel. This allows the spectra to be conformationally averaged. Not available if Simulate Boltzmann-averaged spectra only is selected for NMR spectra.

Search Options link

Click this link to display a pane of options for the conformational search. These options are only available if the Use conformational search option is selected.

Method option menu

Choose a conformational search method. The methods are described in detail in MacroModel Conformational Searches.

Number of steps text box

Specify the number of steps performed in the search. When the number of generated trial structures matches the value in field, the conformational search is terminated.

MM energy window text box

Specify the threshold value for comparison of trial structures. New structures that are generated and minimized are kept only if their energy is less than this value above the current global minimum. Lowering this value results in fewer structures saved.

Max conformers retained text box

Specify the maximum number of conformers to keep for each input structure.

QM Screening settings (for conformer retention)

Specify cutoffs for eliminating redundant conformers after the set generated by MacroModel is minimized by Jaguar.

  • Max atom deviation—consider structures to be different if the maximum atom deviation for any pair of corresponding atoms exceeds the threshold given in the text box, in angstroms.

  • QM energy window—keep conformers only if their QM energy is less than this value above the current global minimum.

Force field option menu

Choose the force field for the conformational search. The choices are OPLS_2005 and OPLS4.

Use customized version option

Use your customized version of the OPLS4 force field, rather than the standard version in the distribution. Only available when you choose OPLS4 from the Force field option menu and you have the appropriate license. This option is set by default to the value of the Use custom parameters by default option in the Preferences panel, under Jobs - Force field, when the current panel is opened. The default directory for the customized version can also be specified as a preference, in the same location.

If the customized version is missing or invalid, the text of this option turns orange and an orange warning icon is displayed to the right, with a tooltip about the problem.

Parameter set button

Select the set of custom parameters for the OPLS4 force field. Opens the Set Custom Parameters Location Dialog Box. Only available when you choose OPLS4 from the Force field option menu and you have the appropriate license.

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.

If the basis set is not available for any of the structures in the Structures table, the cell in the Basis Set column for that structure is colored red. If a composite method is chosen in the Theory text box, the corresponding pre-defined basis set is automatically selected, and the Basis set text box cannot be modified.

See Basis Sets for information on the basis sets available.

Skip geometry optimization of input structures option

Select this option to preserve the geometries of the input structures. This may be useful when comparing spectra for a set of conformers. If using this option for VCD or IR spectra, the input structures must previously optimized.

Solvent option menu

Choose the solvent to be used. The solvent is modeled by a dielectric continuum in which the solute occupies a cavity. The available solvents are water, chloroform, ethanol, methanol, DMSO, and acetonitrile. You can choose None to run the calculation in the gas phase.

If NMR is selected from the Calculate spectra option menu, the Solvent option menu is only available for 13C and 1H. You can calculate 13C and 1H chemical shifts in chloroform, DMSO, or water.

Keywords text box

Specify gen section keywords for the Jaguar calculations. The same keywords are used for all calculations. You might want to specify the basis set and the method in this section, for example. Some keywords are set automatically, such as the keywords for generating VCD and ECD spectra. For information on the keywords, see the The gen Section of the Jaguar Input File.

Job toolbar

Manage job submission and settings. See Job Toolbar for a description of this toolbar.

The Job Settings button opens the Jaguar Spectroscopy - Job Settings Dialog Box, where you can make settings for running the job.

Status bar

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. You can also reset the panel from the Job toolbar.

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.

Tutorials

Related Topics

Workflow Examples

Example input structure file (wflow-spectroscopy_vcd-0001.mae):

{ 
 s_m_m2io_version
 :::
 2.0.0 
} 

f_m_ct { 
 s_m_title
 i_m_Molecular_charge
 i_m_Spin_multiplicity
 i_m_ct_format
 :::
 Structure1 
  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_residue_number
  i_m_color
  i_m_atomic_number
  s_m_color_rgb
  s_m_atom_name
  i_m_minimize_atom_index
  :::
  1 3 -1.593359 -1.026400 -2.195457 1 24 6 808080  "C1"  1
  2 3 -0.565628 -0.480762 -1.202775 1 2 6 A0A0A0  "C2"  2
  3 41 -1.560211 -0.493430 -3.146939 1 21 1 FFFFFF  ""  3
  4 41 -2.606114 -0.944213 -1.799475 1 21 1 FFFFFF  ""  4
  5 41 -1.413367 -2.081553 -2.404048 1 21 1 FFFFFF  ""  5
  6 41 -0.588336 -1.025736 -0.256676 1 21 1 FFFFFF  ""  6
  7 26 0.749607 -0.520029 -1.779849 1 43 7 5757FF  "N7"  7
  8 16 -0.772232 0.882337 -0.969039 1 70 8 FF2F2F  "O8"  8
  9 42 -1.525474 1.167314 -1.465735 1 21 1 FFFFFF  ""  9
  10 43 1.354087 0.054715 -1.209072 1 21 1 FFFFFF  ""  10
  11 43 1.121596 -1.457737 -1.735619 1 21 1 FFFFFF  ""  11
  :::
 } 
 m_bond[10] { 
  # 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
  5 2 6 1
  6 2 7 1
  7 2 8 1
  8 7 10 1
  9 7 11 1
  10 8 9 1
  :::
 } 
}

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

$SCHRODINGER/jaguar run spectroscopy.py -jobname=wflow_spectroscopy_vcd_0001 -vcd -forcefield OPLS4 -conf_search_method mixed -conf_search_steps 200 -mm_energy_window 5.0 -outconfs 100 -max_atom_dev 0.5 -qm_energy_window 5.0 -solvent None -k=dftname=b3lyp-d3 '-k=basis=lacvp**' -k=iacc=1 wflow-spectroscopy_vcd-0001.mae

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

Files generated with release version: 2025-4

Input structure: wflow-spectroscopy_vcd-0001.mae
Output files

Example input structure file (wflow-spectroscopy_ecd-0001.mae):

{ 
 s_m_m2io_version
 :::
 2.0.0 
} 

f_m_ct { 
 s_m_title
 i_m_Molecular_charge
 i_m_Spin_multiplicity
 i_m_ct_format
 :::
 Structure1
  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_residue_number
  i_m_color
  i_m_atomic_number
  s_m_color_rgb
  s_m_atom_name
  i_m_minimize_atom_index
  :::
  1 3 -1.593359 -1.026400 -2.195457 1 24 6 808080  "C1"  1
  2 3 -0.565628 -0.480762 -1.202775 1 2 6 A0A0A0  "C2"  2
  3 41 -1.560211 -0.493430 -3.146939 1 21 1 FFFFFF  ""  3
  4 41 -2.606114 -0.944213 -1.799475 1 21 1 FFFFFF  ""  4
  5 41 -1.413367 -2.081553 -2.404048 1 21 1 FFFFFF  ""  5
  6 41 -0.588336 -1.025736 -0.256676 1 21 1 FFFFFF  ""  6
  7 26 0.749607 -0.520029 -1.779849 1 43 7 5757FF  "N7"  7
  8 16 -0.772232 0.882337 -0.969039 1 70 8 FF2F2F  "O8"  8
  9 42 -1.525474 1.167314 -1.465735 1 21 1 FFFFFF  ""  9
  10 43 1.354087 0.054715 -1.209072 1 21 1 FFFFFF  ""  10
  11 43 1.121596 -1.457737 -1.735619 1 21 1 FFFFFF  ""  11
  :::
 } 
 m_bond[10] { 
  # 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
  5 2 6 1
  6 2 7 1
  7 2 8 1
  8 7 10 1
  9 7 11 1
  10 8 9 1
  :::
 } 
}

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

${SCHRODINGER}/jaguar run spectroscopy.py -jobname=wflow_spectroscopy_ecd_0001 -ecd -forcefield OPLS4 -conf_search_method mixed -conf_search_steps 200 -mm_energy_window 5.0 -outconfs 100 -max_atom_dev 0.5 -qm_energy_window 5.0 -solvent None -k=dftname=b3lyp-d3 '-k=basis=lacvp**' -k=iacc=1 wflow-spectroscopy_ecd-0001.mae

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: wflow-spectroscopy_ecd-0001.mae
Output files

Note: The quantum mechanical calculations are performed in gas phase but the NMR chemical shift parameterization corresponds to chloroform.

Example input structure file (wflow-spectroscopy_nmr-0001.mae):

{ 
 s_m_m2io_version
 :::
 2.0.0 
} 

f_m_ct { 
 s_m_title
 i_m_Molecular_charge
 i_m_Spin_multiplicity
 i_m_ct_format
 :::
 Structure1 
  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_residue_number
  i_m_color
  i_m_atomic_number
  s_m_color_rgb
  s_m_atom_name
  i_m_minimize_atom_index
  :::
  1 3 -1.593359 -1.026400 -2.195457 1 24 6 808080  "C1"  1
  2 3 -0.565628 -0.480762 -1.202775 1 2 6 A0A0A0  "C2"  2
  3 41 -1.560211 -0.493430 -3.146939 1 21 1 FFFFFF  ""  3
  4 41 -2.606114 -0.944213 -1.799475 1 21 1 FFFFFF  ""  4
  5 41 -1.413367 -2.081553 -2.404048 1 21 1 FFFFFF  ""  5
  6 41 -0.588336 -1.025736 -0.256676 1 21 1 FFFFFF  ""  6
  7 26 0.749607 -0.520029 -1.779849 1 43 7 5757FF  "N7"  7
  8 16 -0.772232 0.882337 -0.969039 1 70 8 FF2F2F  "O8"  8
  9 42 -1.525474 1.167314 -1.465735 1 21 1 FFFFFF  ""  9
  10 43 1.354087 0.054715 -1.209072 1 21 1 FFFFFF  ""  10
  11 43 1.121596 -1.457737 -1.735619 1 21 1 FFFFFF  ""  11
  :::
 } 
 m_bond[10] { 
  # 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
  5 2 6 1
  6 2 7 1
  7 2 8 1
  8 7 10 1
  9 7 11 1
  10 8 9 1
  :::
 } 
}

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

${SCHRODINGER}/jaguar run spectroscopy.py -jobname=wflow_spectroscopy_nmr_0001 -nmr -nmr_types 1H 13C -only_average_nmr -forcefield OPLS4 -conf_search_method mixed -conf_search_steps 200 -mm_energy_window 5.0 -outconfs 100 -max_atom_dev 0.5 -qm_energy_window 5.0 -solvent None -k=dftname=b3lyp-d3 '-k=basis=lacvp**' -k=iacc=1 wflow-spectroscopy_nmr-0001.mae

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

Files generated with release version: 2025-4

Input structure: wflow-spectroscopy_nmr-0001.mae
Output files