Jaguar - pKa Panel

Jaguar pKa, Jaguar pKa, micro pka, micropka, macro-pka, macro pka, macropka, macro-pka

The Jaguar - pKa panel allows you to perform quantum-mechanical calculations of the pKa of one or more molecules.

To open this panel, do one of the following:

  • Click the Tasks button and browse to Ligand Preparation and Library Design → Quantum-Mechanical
  • Click the Tasks button and browse to Quantum Mechanics → pKa
  • Click the Tasks button and browse to Jaguar → pKa
  • Click the Tasks button and browse to Materials → Quantum Mechanics → Molecular Quantum Mechanics → More Molecular QM Tasks → pKa
  • Overview
  • Using
  • Features
  • Additional Resources
  • Examples

Overview of pKa Calculations

Two modules are available in Jaguar for the prediction of pKa: Jaguar pKa and Macro-pKa.

Jaguar pKa

The Jaguar pKa module is appropriate for molecules whose protonation states can be straightforwardly defined. For example:

  • Molecules with only one protonatable/deprotonatable functional group and no likely tautomers.

  • Molecules with several protonatable/deprotonatable functional groups, but it is certain that these groups participate in protonation equilibria in different pH ranges. In other words, the micro-pKa’s of these groups are “well-separated”, with the micro-pKa difference being 2-3 and larger. You should be certain which of the functional groups with well-separated pKa’s is responsible for the pKa signal observed in the experiment, if comparison with the experiment is planned.

The workflow involve geometry optimization of the protonated and deprotonated species, single-point energy and frequency calculations, and an empirical correction. The accuracy (RMSD) of the prediction is in the range 0.2-0.5 pKa units for bases, and 0.2-1.0 pKa units for acids, depending on the functional group. Empirical corrections have been generated for a wide range of functional groups, including some zwitterions. For groups that are not covered by the specific functional group (specified by SMARTS), more general functional groups are also used, with a larger error in the predicted pKa. The output reports the pKa for all of the functional groups matched, and reports the most accurate value in the Maestro property. The entropic correction for equivalent sites is included in the prediction.

If you want to calculate pKa values without the empirical correction, you can add ipkaraw=1 to the gen section of the input file. The errors in the raw pKa calculations are much higher. You might want to do this, for example, to develop your own empirical correction.

For more information on Jaguar pKa, please see The Jaguar pKa Prediction Module.

Macro pKa

Note: The Macro-pKa module requires a Macro-pKa license in addition to the Jaguar license.

The Macro-pKa module can handle the cases covered by Jaguar pKa, but is also appropriate for more complex systems, including:

  • Molecules with several protonatable/deprotonatable functional groups whose dissociations may not occur in clearly separated pH regions.

  • Molecules with many protonatable/deprotonatable groups and potentially multiple protonation states.

  • Molecules prone to tautomerism.

The Macro-pKa workflow involves automatic tautomer generation and selection of protonatable/deprotonatable functional groups, geometry optimization of the protonated and deprotonated species, single-point energy and frequency calculations, empirical corrections, and the calculation of macro-pKa from micro-pKas. Macro-pKa results are directly comparable to experimentally measured pKas.

Macro-pKa calculations should be easier to set up than Jaguar pKa calculations, since you do not have to manually identify protonation/deprotonation sites. User mistakes are also less common when setting up Macro-pKa calculations. A downside to using Macro-pKa is its potentially higher computational cost. Macro-pKa computes micro-constants for all reasonable tautomers, as opposed to Jaguar pKa, which focuses on a tautomeric equilibrium or a few manually selected equilibria.

For more information on Macro pKa, please see Introduction to Macro-pKa.

Using the Jaguar - pKa Panel

The Jaguar panel for pKa prediction has only the Input, SCF, and Solvent tabs, because all other input is predefined.

To read in an input file, click the arrow next to the Settings button () and choose Read. The panel automatically recognizes which pKa prediction method is intended by the file. The subsections below describe how to set up calculations for micro and macro pKa calculations.

Jaguar pKa

To run the Jaguar pKa module, choose Jaguar pKa (Micro-pKa) as the pKa prediction method. After selecting structures, you must designate one or more atoms in each molecule as the acidic or basic sites for which the pKa is evaluated. The atom you choose for any site must be the hydrogen atom in an acid, or the basic atom in a base. To designate the sites, click in the appropriate pKa Atom cell. You can then either enter the atom names or pick the atoms in the Workspace. If the structure is not already in the Workspace, it is placed in the Workspace (as the only structure).

If you want to perform a conformational search on the protonated and the deprotonated species with MacroModel before the pKa calculation is performed, select Perform conformational searches on input structures. The lowest-energy conformer is used for each species by default in a microscopic pKa calculation, but you can set an energy window and a maximum number for selection of multiple conformers for macroscopic pKa calculations (which only consider conformers, not tautomers). For a more thorough conformational search, select Thorough for Accuracy. This will give better results for molecules with many conformations. This option requires a MacroModel license.

If you want to calculate pKa values in DMSO (e.g. for carbon acids), you can choose DMSO from the Solvent option menu in the Solvent tab.

Usually it is not necessary to change any of the SCF convergence settings, but if you want to, you can do so in the SCF tab.

When you have selected the structures and pKa atoms, and made any settings, click Run.

The results of a pKa calculation are returned as a table in the output text file (.out), and property values are added to the output structure, which is obtained by optimizing the geometry of the input structure. The pKa atoms have the pKa value as an atom property, (pKa water) and the structure has the pKa value of the first pKa atom as an entry property.

When Jaguar pKa (Micro-pKa) is chosen, this edit can be used to add standard Jaguar keywords to the input files.

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 jaguar_pka Command Help.

Macro pKa

To run the Macro-pKa module, choose Macro-pKa as the pKa prediction method. If you want to explore the macro-pKa transitions within a certain range, select pKa from the Set range for option menu, and set the range of pKa's to consider. If you want to explore the macro-pKa transitions between a number of charged species, starting from a single molecule, select Relative Charge from the Set range for option menu, and set the range of relative charges to consider. Please see the Input tab for more information on these settings.

We do not recommend changing the SCF convergence settings.

If you want to perform a conformational search with MacroModel for each tautomer included in the calculation, select Perform conformational searches on input structures. The lowest energy conformers for each tautomer, up to the number set in the Max number of conformers to use for each species text box, are included in the Macro-pKa calculation. This option requires a MacroModel license.

Any keywords provided in the Keywords text box should be Macro-pKa keywords only.

Macro-pKa predictions can only be performed for systems containing a single molecule. Every row in the table launches a separate Macro-pKa calculation. If multiple entries are selected for Macro-pKa prediction, an input file is written for each entry in the job directory, and one submission script (.sh) is used to run all the jobs. The job files for each entry are written to its own subdirectory.

To visualize the results of a Macro-Pka calculation, use the Workflow Action Menu to open a page containing a breakdown of populations at different charges (at a specific pH), a graph of tautomer populations as a function of pH, and a list of SMILES strings for each tautomer. See Results of a Macro-pKa calculation 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 macro_pka.py Command Help.

Jaguar - pKa Panel Features

  • Input
  • SCF
  • Solvent

Input Tab Features

Use structures from option menu

Choose the structure source for the current task.

  • 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 (n included entries)—Use the entries that are currently included in the Workspace, treated as separate structures. The number of entries in the Workspace is shown on the menu item. An icon is displayed to the right which you can click to open the Project Table and include or exclude entries.
Open Project Table button

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

pKa prediction method options

For more information on the difference between Jaguar pKa and Macro-pKa, please see Jaguar - pKa Panel.

Jaguar pKa (Micro-pKa) option

Calculate the pKausing the Jaguar pKa prediction module. Please see Jaguar - pKa Panel for more information.

Find pKa atoms using option and menu

Find pKa atoms in the molecule, rather than specifying them manually. The menu offers the following choices:

  • Automatic search—automatically identify pKa atoms in the molecules, and run a pKa calculation for each. Sets ipkasearch=all. The pKa Atom column in the Structures table is disabled and the text reads auto-search.

  • SMARTS—specify one or more SMARTS patterns to identify pKa atoms. Opens a pane in which you can type in the SMARTS pattern or generate one from the Workspace selection (Get from Selection), specify the pKa atom indices in the SMARTS pattern, define another pattern (Define Another) and step through patterns (arrow buttons). A Define button is placed next to the menu so you can reopen the pane to change the definitions. When you close the pane, the SMARTS search is run and the atoms found are entered in the pKa Atom column of the table. A pKa calculation is run for each atom identified by the SMARTS patterns.

    The SMARTS patterns remain defined for the Maestro session, and are used again the next time you choose this option.

Perform conformational searches on input structures (requires MacroModel) option

Run a conformational search on each of the input structures, in both protonated and deprotonated forms, with MacroModel (-csrch command option).

Accuracy options

Select an option for the accuracy level of the conformational search (ipka_csrch_acc):

  • Fast—Requests 100 conformers from the MacroModel conformational search. If the molecule has more than 5 rotatable bonds, this could be insufficient to produce the lowest conformer.
  • Thorough—Requests 3000 conformers from the MacroModel conformational search, with some other adjustments in parameters to produce a thorough coverage of conformational space.
Max number of conformers to use for each species box

Specify the maximum number of conformers to use for the protonated and for the deprotonated form of the molecule (ipka_max_conf). The conformer selection starts from the lowest energy conformer, and is subject to the conformational energy window. If you specify a single conformer (the default), the lowest-energy conformer is taken for each species, and a microscopic pKa calculation is run. If you specify multiple conformers, a macroscopic a pKa calculation is run using all the conformers—see Conformational Flexibility in Jaguar pKa Calculations for details on how the calculation is done.

Conformational energy window text box

Specify the maximum energy of any conformer selected, relative to the lowest energy conformer (ipka_erg_window). Conformers whose energy is above this threshold are not included.

Allow use of zwitterion functional groups option

Use specific functional group patterns and corrections for zwitterions. If this option is deselected, the generic zwitterion patterns are used instead.

Macro-pKa option

Calculate the pKausing the Macro-pKa prediction module. Please see Jaguar - pKa Panel for more information on the module.

Set range for option menu and Min/Max text boxes

Select how you want to define the macro-pKa transitions to consider in the calculation. The range set using the Min and Max text boxes are applied to all structures listed in the Structures table. You can specify a custom range for a molecule by directly editing the cells in the table.

  • pKa— Define macro-pKa transitions by setting a pKa range (pka_max and pka_min). The default range of 2.0 to 12.0 min is sufficient for most systems, but there is no restriction on the range value. See Defining Charge Transitions.

  • Relative Charge—(relative_charges)- Define macro-pKa transitions by setting a range of charges relative to the charge of the molecule. For example, if a molecule has a total charge of 2, and you would like to calculate the macro-pKa transitions of total charges 5 → 4, 4 → 3, 3 → 2, and 2 → 1, set the Minrelative charge as -1 (1 - 2) and Maxrelative charge as 3 (5 – 2).

Perform conformational searches on input structures (requires MacroModel) option

Run a conformational search on each automatically generated tautomer considered in the Macro-pKa calculation. The lowest energy conformers for each tautomer, up to the number set in the Max number of conformers to use for each species text box, are included in the Macro-pKa calculation. This option requires a MacroModel license.

Max number of conformers to use for each species text box

Specify the maximum number of lowest energy conformers for each tautomer to include in the Macro-pKa calculation (csrch). We recommend doing a conformational search with N=2-5 per generated tautomer for larger and more flexible molecules.

Structures table

This table lists the entries in the Project Table that are used as the input structures for the job, according to the choice from the Use structures from option menu. To change the structures used for the calculation, you can change the selected structures or included structures in the Project Table panel or the Entry List panel. You can double-click in a cell to edit the values (ID, In, and Entry Title columns are not editable). The columns of the table may be different depending on the calculation type, and include:

  • ID—The entry ID of the structure.
  • In—Use this column to display the structures in the Workspace, just as in the Project Table panel or the Entry List panel. If you chose Workspace as the source of structures, excluding structures from the Workspace (clearing the In box) removes them from the table.
  • Entry Title—The entry title of the structure.
  • Charge—Specify the charge (molchg in the gen section). Default is 0 and is displayed in italics. The value is stored as a Maestro property.
  • Spin Mult.—Specify the spin multiplicity (multip in the gen section). Default is 1 (singlet) and is displayed in italics. If you use the spin-orbit ZORA Hamiltonian, spin is no longer conserved, and the multiplicity is only related to the number of electrons (1 for even, 2 for odd). The value is stored as a Maestro property.
  • pKa Atom (Add H+) and pKa Atom (Remove H+)—Only present if Jaguar pKa (Micro-pKa) is selected. You can choose one or more pKa atoms in any structure, by entering the atom names in the pKa Atom cells or picking the atoms in the Workspace. If you pick multiple atoms, a separate pKa calculation is run for each atom as a subjob of the main job. The atoms that are added to the pKa Atom (Remove H+) column must be hydrogen atoms. The atoms that are added to the pKa Atom (Add H+) column must be nonhydrogen atoms, for which the calculated pKa is that of the conjugate acid (protonated form).
  • Min pKa and Max pKa/Min Relative Charge and Max Relative Charge—Only present if Macro-pKa is selected. The column header is determined by what is selected in the Set range for option menu. Double-click in a cell to set custom Min and Max values for each entry in the table, which overrides the values specified from the Min and Max text boxes above the table.
  • Active Atoms— Only present if Macro-pKa is selected. If you have a good guess of which protons and heavy atoms will be involved in tautomerization processes for the given molecule, you can specify the “active atoms” (active_atoms) that Macro-pKa should consider in its generation of tautomers. This can significantly reduce the number of tautomers considered. Double-click in a cell to choose one or more active atoms for the entry by entering the atom names in the cell or picking the atoms in the Workspace. The cell turns red if an invalid atom name is entered.

SCF Tab Features

In this tab you set the parameters that control the SCF convergence. Keywords for the gen section of the input file that correspond to the controls in this tab are given in parentheses.

Accuracy level option menu

Set the accuracy for pseudospectral calculations, or turn off the pseudospectral method.

  • Quick— Use mixed pseudospectral grids with loose cutoffs (Sets iacc=3).
  • Accurate— Use mixed pseudospectral grids with accurate cutoffs (Sets iacc=2).
  • Ultrafine— Use ultrafine pseudospectral grids with tight cutoffs (Sets iacc=1).
  • Fully analytic— Perform a fully analytic calculation: turn off the pseudospectral method (Sets nops=1). Can be run in parallel with OpenMP threads—see Running a Multithreaded Jaguar Job with OpenMP.

For more information on grids and cutoffs, see The Grid File for Jaguar Calculations and The Cutoff File for Jaguar Calculations.

Initial guess option menu

Choose the method for generating an initial guess for the molecular orbitals.

  • Atomic overlap—Construct a guess for the molecular orbitals from atomic orbitals (iguess=10). The core orbitals are set to the atomic core orbitals. The overlap matrix is diagonalized in the space of the valence atomic orbitals, and the eigenvectors with the largest eigenvalues are taken for the valence orbitals. The entire set is orthogonalized core first, then valence. This is the default.

  • Atomic density—Construct a guess from a superposition of atomic densities (iguess=11). The density is projected onto the AO basis. The resulting matrix is diagonalized to give natural orbitals, which are used as the initial guess orbitals.

  • Core Hamiltonian—Generate an initial guess by diagonalizing the one-electron Hamiltonian matrix (iguess=0). This is rarely a good guess, as the orbitals are usually too tight.

  • Ligand field theory—For transition metal complexes, use ligand field theory to construct an initial guess for the metal d orbitals. (iguess=25) An effective Hamiltonian is diagonalized, taking into account the assigned formal charges on the metal and the ligand and the occupation of the ligand orbitals, to determine the d-orbitals and the orbital ordering. The core and ligand orbitals are determined from the atomic orbitals using the atomic overlap.

  • Ligand field theory with d-d repulsion—For transition metal complexes, use ligand field theory including d-d repulsion to construct an initial guess (iguess=30). The procedure is the same as above, except that repulsion between the d electrons on the metals is included to determine the orbital ordering and hence the occupation of the d orbitals and the spin state.

Convergence criteria section

In this section you set the criteria for convergence of the SCF process.

Maximum iterations text box

Specify the maximum number of SCF iterations in this text box (maxit). The default value is 48. The absolute maximum allowed is 5000.

Energy convergence text box

Specify the SCF energy convergence threshold in this text box (econv). The default value is 5.0x10-5 Eh.

RMS density matrix change text box

Specify the SCF density convergence threshold in this text box. This value is the maximum change in the RMS density difference between iterations. (dconv). The default value is 5.0x10-6.

Convergence methods section

In this section you choose the methods used to enhance or control convergence.

SCF level shift text box

Specify the level shift for the virtual orbitals (vshift). The default value is 0.0 for non-metallic systems and Hartree-Fock calculations. For DFT calculations on metallic systems the default is 0.2 for hybrid functionals, 0.3 for pure functionals.

Thermal smearing option menu

Select the thermal smearing method for convergence control (ifdtherm). The menu options are:

  • None— Do not use thermal smearing (ifdtherm=0).
  • FON— Fractional occupation number method (ifdtherm=1).
  • pFON— Pseudo-fractional occupation number method (ifdtherm=2).

See the Jaguar User Manual for details of this method.

Initial temperature text box

Set the initial temperature for thermal smearing. (fdtemp in the gen section of the input file). The initial temperature text box is only available if you choose an item other than None from the Thermal smearing option menu.

Convergence scheme option menu

Choose the SCF convergence acceleration scheme (iconv).

  • DIIS— Use the DIIS convergence scheme (iconv=1).
  • OCBSE— Use the OCBSE convergence scheme (iconv=3).
  • GVB-DIIS— Use the GVB-DIIS convergence scheme (iconv=4).
  • Other— Selected if the input file uses another convergence scheme, otherwise unavailable.

For more information on these convergence schemes, see the Jaguar User Manual.

Force convergence option

Attempt to force convergence by adding level shift and decreasing it during iterations, fixing the number of canonical orbitals, and running at ultrafine accuracy (vshift, iacscf=1).

Compute wave function stability option

Perform wave function stability analysis (wf_stability = 1). Eigenvalues of the diagonalized molecular orbital Hessian are reported.

Orbitals section

Set options relating to the orbital occupations, canonicalization, and localization.

Fixed symmetry populations option

Fix the number of electrons in each irreducible representation (ipopsym=1).

Use consistent orbital sets when all input structures are isomers option

When performing calculations on a set of isomers, taken either from the project table or from a file, select this option to ensure that all calculations use the same number of canonical orbitals. This ensures consistency of the calculations and enables the results to be validly compared.

This option is not present in the Jaguar - Reaction panel, as the structures are not isomeric.

Final localization option menu

Choose the localization method for the valence orbitals from this option menu (locpostv).

  • None— Do not localize final valence orbitals (locpostv=0). This is the default.
  • Pipek-Mezey— Perform Pipek-Mezey localization, maximizing Mulliken atomic populations (loclpostv=2).
  • Boys— Perform Boys localization (loclmp2c=1).
  • Pipek-Mezey (alt) Perform Pipek-Mezey localization, maximizing Mulliken basis function populations (locpostv=3).

Solvent Tab Features

In this tab you choose a solvent from a predetermined set for pKa calculations. The solvent is included in the calculation as a dielectric continuum with a cavity for the molecule.

Solvent pKa option menu

Choose the solvent for the calculation of the pKa values from this option menu.There are only two choices, Water and DMSO, as these are the only solvents for which pKa parameters are available. The default is Water.

This solvent is used only for the calculations at the final geometries that are used to determine the pKa, unless you select Use solvation for geometry optimization step.

Use solvation for geometry optimization step option

Run the geometry optimization in the selected solvent, rather than in the gas phase (the default). This option generally yields more accurate pKa values, but is slower than gas-phase optimization.

Keywords text box

Enter keywords and macros for the gen section. These keywords and macros override settings made elsewhere in the panel. They do not appear in the input file when you edit it with the Edit Job Dialog Box, but are added to the gen section when the file is written out on clicking Run. For more information on the keywords you can use, see 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 pKa - 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

Note: Sites to remove H+ or add H+ are specified by ipkasites keyword. Comma delimited lists denote each atom to assess. Can also perform an automated search of potential basic atoms or acidic hydrogens by setting ipkasites=all. To model a sequential dissociation (pKa2) you would have to start with a singly dissociated molecule in the workspace.

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

&gen
ipka_prot_deprot=both
ipkasites=H5
ipka_lower_cut=2.0
ipka_upper_cut=6.0
ipka_solv_opt=1
ipka_max_conf=3
ipka_csrch_acc=0
&
&zmat
C1     -0.4163000000000   0.5181000000000   2.4848000000000
O2      0.5557000000000   1.2181000000000   2.6175000000000
H3     -1.2388000000000   0.4240000000000   3.2102000000000
O4     -0.6643000000000  -0.2721000000000   1.4224000000000
H5      0.0829000000000  -0.1601000000000   0.8080000000000
&

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

$SCHRODINGER/jaguar run pka.py -n -csrch -jobname=wflow-pka_jaguar-0001 wflow-pka_jaguar-0001.in

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 file: wflow-pka_jaguar-0001.in
Output files

Note: The pKa predictions were assessed in the range of 2-12, according to defaults.

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

csrch = 2
infile = wflow-pka_macro-0001.mae

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

{ 
 s_m_m2io_version
 :::
 2.0.0 
} 

f_m_ct { 
 s_m_title
 i_m_ct_enhanced_stereo_status
 s_m_entry_id
 s_m_entry_name
 b_sd_chiral_flag
 i_sd_version
 s_m_Source_Path
 s_m_Source_File
 i_m_Source_File_Index
 i_m_ct_format
 :::
 Structure1 
  0
  1 
  pyr.1 
  0
  0
  /Users/moore1 
  pyr.xyz 
  1
  2
 m_atom[10] { 
  # 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
  :::
  1 25 -1.197600 1.984000 -0.094600 900 43 7 5757FF 
  2 2 -0.019800 1.395800 -0.069000 900 2 6 A0A0A0 
  3 2 1.196700 2.074200 -0.035000 900 2 6 A0A0A0 
  4 2 1.093800 3.460700 -0.029300 900 2 6 A0A0A0 
  5 25 -0.083900 4.104900 -0.054600 900 43 7 5757FF 
  6 2 -1.165400 3.324700 -0.086000 900 2 6 A0A0A0 
  7 56 -0.016400 0.060300 -0.076800 900 8 9 00FF7F 
  8 41 2.143300 1.549000 -0.014700 900 21 1 FFFFFF 
  9 41 1.987200 4.080800 -0.003600 900 21 1 FFFFFF 
  10 41 -2.129800 3.826200 -0.106900 900 21 1 FFFFFF 
  :::
 } 
 m_bond[10] { 
  # First column is bond index #
  i_m_from
  i_m_to
  i_m_order
  :::
  1 1 6 2
  2 1 2 1
  3 2 3 2
  4 2 7 1
  5 3 4 1
  6 3 8 1
  7 4 9 1
  8 4 5 2
  9 5 6 1
  10 6 10 1
  :::
 } 
}

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

$SCHRODINGER/jaguar run macro_pka.py -jobname=wflow_pka_macro_0001 wflow-pka_macro-0001.in

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

Files generated with release version: 2026-1

Input file: wflow-pka_macro-0001.in
Input structure: wflow-pka_macro-0001.mae
Output files