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, and final macro-pK_a’s

• <jobname>_populations.mae— contains 3D structures of the lowest energy conformations of the tautomers

• <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. 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.