Macro-pKa Output Files and Directories

There are several useful output files and directories produced by a Macro-pKa calculation:

• <jobname>.out— gives full details about tautomers generated (SMILES strings, tautomer populations), energies, final macro-pK_a’s, and the isoelectric pH if applicable

• <jobname>_populations.mae— contains 3D structures of the lowest energy conformations of the tautomers. If the molecule has both positively and negatively charged protonation states, the isoelectric pH is included as an entry property.

• <jobname>_micro_pkas.mae— contains the most important micro-pKa transitions micro-pK_a’s along with the associated tautomers 3D structures

• <jobname>_final_results_figure/<jobname>_populations.html— an html 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. If applicable, the isoelectric pH is shown as a dashed vertical line on the tautomer populations graph. The file opens into a browser. See Results of a Macro-pKa calculation.

Note

The empirical correction directory is only produced if you use the Jaccard similarity method for empirical corrections.

• <jobname>_empirical_corrections— this directory contains the details of every micro-pK_a calculation in its own subdirectory (pka_<n>). Each pka_<n> directory contains:

  • empirical_corrections.html— an html page containing a breakdown of the empirical correction used for obtaining micro-pK_a from raw pK_a. See Breakdown of Empirical Corrections

  • dynamic_cluster.csv— a spreadsheet with information on the training data used to calculate the empirical correction with a dynamic fitting, including the SMILES string, raw pK_a, and adjusted experimental pK_a. See Applying Empirical Corrections for pKa Calculations.