Jaguar Input Files for pK_a Calculations

Overview
Examples

You can prepare a Jaguar input file for a pK_a calculation using a text editor. The input file must contain a molecular geometry and a labeled pK_a atom. The pK_a atom is either an acidic hydrogen in acids or conjugate acids, or a non-hydrogen atom to be protonated in bases or conjugate bases.

The pK_a atom can be marked by setting the gen section keyword ipkat to either the atom’s name, or to the atom’s order number in the zmat section.

Here are two equivalent input file examples for formic acid:

&zmat
  C1   1.0590559100      0.0794463600      0.3608319800
  O2   0.8609619100      1.1054614700     -0.2390046100
  O3   2.2130316700     -0.6129886300      0.3489813100
  H1   2.8258867600     -0.1221771000     -0.2269021000
  H2   0.3281776900     -0.4358328800      1.0011835800
&
&gen
ipkat=H1
&
 
&zmat
  C1   1.0590559100      0.0794463600      0.3608319800
  O2   0.8609619100      1.1054614700     -0.2390046100
  O3   2.2130316700     -0.6129886300      0.3489813100
  H1   2.8258867600     -0.1221771000     -0.2269021000
  H2   0.3281776900     -0.4358328800      1.0011835800
&
&gen
ipkat=4
&

When the pK_a job is run, Jaguar checks that the functional group containing the designated pK_a atom has correction parameters available. If it does not, the job fails immediately, and an error message explaining the problem is printed to jobname.out.

If you want to calculate a raw pK_a value using the Jaguar methods but without correction factors, you can set ipkaraw=1 in the gen section of the input file. You might want to do this when developing your own correction factors (see Developing Your Own Jaguar pKa Correction Parameters).

You can generate multiple conformers for the protonated and deprotonated species, and calculate a macroscopic pK_a value making use of these conformers (method 2 in Conformational Flexibility in Jaguar pKa Calculations). To generate multiple conformers, set ipka_max_conf to the maximum number of conformers, and include the -csrch option when you run jaguar pka. You can also set an energy window (in kcal/mol) for filtering out conformers, with the ipka_erg_window keyword. Conformers are discarded if their energy relative to the lowest energy conformer is higher than the specified value. If you want a faster search with fewer conformers, you can set ipka_csrch_acc to 0. You can also turn on solvation in the optimization of the conformers with Jaguar by setting ipka_solv_opt to 1. The default is gas-phase optimization, but use of solvation can help in some cases. See pKa Keywords in the Jaguar Input File for information on the default values and settings made by these keywords.

Setting ipkaverbose=1 produces more output, including intermediate pK_a(i,j) values. When running the job, subjobs for each conformer can be distributed over multiple processors.

You can run pK_a calculations on multiple sites in the same molecule, by adding the ipkasites keyword to the gen section. The value for this keyword is a comma-separated list of atom numbers or atom labels, with no spaces, that identify the pK_a atoms. You can mix atom numbers and atom labels, e.g. ipkasites=3,H5,O2,7. The job is run as separate pK_a calculations with a single pK_a atom in each, and the results are collected at the end. The output structure has the pK_a values for each pK_a atom stored as an atom property (r_j_pKa_water), and the pK_a value for the first pK_a atom stored as an entry property (also named r_j_pKa_water).

You can turn off the entropic correction for equivalent sites by setting ipkasymm=0 in the gen section of the input file. By default it is set to 1, to include the entropic correction. To print the entropic correction, set ipkaverbose=1 in the gen section; by default it is set to 0 and the correction is not printed separately.

Jaguar Input Files for pKa Calculations

Workflow Examples

Jaguar Input Files for pK_a Calculations