macro_pka_results Command Help

Command: $SCHRODINGER/utilities/macro_pka_results

usage: macro_pka_results [-h] [-jobname JOBNAME]
                                                [-use_jaccard]
                                                [-training_data <training.mae> | -ml_model <dir_path>]
                                                [-pH <X>]
                                                [-gather_results <dir> [<dir> ...]]
                                                [-pka_erg_window <X>]
                                                [-max_active_atoms <N>]
                                                [-image_size <X>]
                                                [-use_cluster_fitting]
                                                [-split_stereoisomers]
                                                [-get_pk50s]
                                                [-nconf_average <N>]

Utility script to call the post-processing in a macro-pKa workflow.

This script assumes a set of protonated and deprotated tautomers and
conformers have been prepared in appropriately named files of
the form charge_*.mae, where the index refers to the total charge
relative to the input structure referenced in the input file.

The structures will be used as-is without further geometry optimization
or QM calculations in the following steps:

(1) Read single-point QM energies for pKa thermodynamic cycle.
(2) Process energies using pKa-on-the-fly algorithm to get micro-pKa's.
(3) Combine micro-pKa's into final macro-pKa and tautomer populations.

options:
  -h, --help            show this help message and exit
  -jobname JOBNAME      name of job, e.g. to name output files
  -use_jaccard          Disable using Ligand-ML machine-learning model, use
                        Jaccard similarity for the empirical corrections.
  -training_data <training.mae>
                        Custom .mae file for empirical training data.
  -ml_model <dir_path>  Custom model directory for Ligand-ML empirical
                        corrections.
  -pH <X>               pH for tautomer populations.
  -gather_results <dir> [<dir> ...]
                        Search and collect results from one or more sub-
                        directories.
  -pka_erg_window <X>   Energy window cut-off per pKa charge-pair in kcal/mol.
  -max_active_atoms <N>
                        Maximum number of active atoms considered when
                        evaluating micro-pKa tautomer pairs.
  -image_size <X>       Scale factor to expand tautomer image size
                        (default=30).
  -use_cluster_fitting  use of cluster fitting method for the empirical
                        corrections.
  -split_stereoisomers  separate stereoisomers when calculating final
                        populations.
  -get_pk50s            compute pK50 values and assign them to input
                        structure.
  -nconf_average <N>    number of conformers to include per species in the
                        generation of micro-pKa's from nano-pKa's