macro_pka.py Command Help

Command: $SCHRODINGER/jaguar run macro_pka.py

usage: $SCHRODINGER/jaguar run macro_pka.py [-h] [-WAIT] [-DEBUG]
                                            [-jobname <name>] [-subdir]
                                            [-recover] [-no_subjob_files]
                                            [-scr <absolute path>]
                                            [-PARALLEL <N>] [-max_threads <T>]
                                            [-procs_per_node <N>]
                                            [-use_one_node | -use_multiple_nodes]
                                            [-HOST <host>:<M>]
                                            [-SUBHOST <host>:<M>] [-SAVE]
                                            [-NOJOBID] [-OPLSDIR <oplsdir>]
                                            infile

Top-level script for Jaguar Macro-pKa workflow.

positional arguments:
  infile                Please specify one Macro-pKa .in file

options:
  -h, --help            show this help message and exit

other options:
  -WAIT                 Wait for job to finish before returning prompt.
  -DEBUG, -D            Print detailed information about job launch.
  -jobname <name>       Set the job name.
  -subdir               Run Jaguar in a sub-directory.
  -recover              Manually re-run a job using the recover mechanism. NOTE this option is not recommended for default recovery jobs.
                        Use "jaguar run <filename>.recover" instead (see documentation for more details).
  -no_subjob_files      Do not return subjob output files to launch directory.
  -scr <absolute path>  Specify a scratch directory (must not already exist). Directory must be given as an absolute path.
                        Note this will be used by the Fortran backend and is independent of the specification of -TMPDIR.
  -PARALLEL <N>         Use up to <N> CPUs simultaneously for the whole workflow, automatically allocated among subjobs, including threaded subjobs.
  -max_threads <T>      Use no more than <T> OpenMP threads for each Jaguar subjob. Default 8.
  -procs_per_node <N>   Use no more than <N> CPUs per node. Default is taken from the schrodinger.hosts file; if undefined 8.
  -use_one_node         Force CPU resources to be requested upfront on one node. 
                        This pool of CPUs will be used for the duration of the job instead of resubmitting to the queue.
  -use_multiple_nodes   Force CPU resources to be requested dynamically from the queue (if available) instead of upfront on one node.

commonly used Schrodinger Suite options:
  -HOST <host>:<M>      Run job remotely on host <hostname>. The optional :<M> defines the maximum number of simultaneous subjobs. 
                        May be combined with -PARALLEL <N>.
  -SUBHOST <host>:<M>   Run any subjobs remotely on subhost <hostname>. The optional :<M> defines the maximum number of simultaneous subjobs. 
                        May be combined with -PARALLEL <N>.
  -SAVE                 Return .zip file of scratch directory.
  -NOJOBID              Run Jaguar interactively without jobserver (not available with python workflows).
  -OPLSDIR <oplsdir>    Use custom FF parameters from specified directory for workflows which support it.

macro_pka Input Keywords:
----------------------------------------
conformer_files: .mae files containing precomputed tautomers and conformers. Note the "relative_charges" keyword still controls which charges are included in a calculation, regardless of the structures provided here. If no tautomers or conformers of a given charge are found in this file, the code will attempt to auto-generate them as usual.
 Default=[]

relative_charges: Included charge states relative to input structure.
 Default=[]

active_atoms: Atom indices of tautomeric active sites.
 Default=[]

chiral_atoms: Atom indices for chiral centers to racemize.
 Default=[]

debug: Print extra debugging information.
 Default=False

protonate: Protonate input structure.
 Default=False

deprotonate: Deprotonate input structure.
 Default=False

qrnn_csrch: Use QRNN to accelerate the filtering of conformers and tautomers.
 Default=True

mlff_csrch: Use MLFF to accelerate the filtering of conformers and tautomers.
 Default=False

use_ml: Use Ligand-ML machine-learning method for the empirical corrections.
If False, use Jaccard similarity method for empirical corrections.
 Default=True

split_stereoisomers: Separate stereoisomers when calculating final populations.
 Default=False

add_stereoisomers: Explicitly add stereoisomers involving pKa-active atoms when auto-generating tautomers.
 Default=True

do_charge_filtering: Filter away auto-generated tautomers if they have an excessive number of separated charges.
 Default=True

csrch: Do conformational search with <N> confs per tautomer, where 0 implies conformational search is skipped. Note these keywords are mutually exclusive: ['csrch', 'autoconf_config']
 Default=0

pka_min: Minimum macro-pKa sweep cut-off value.
 Default=2.0

pka_max: Maximum macro-pKa sweep cut-off value.
 Default=12.0

ph: pH for tautomer populations.
 Default=7.0

infile: Input .mae file containing one structure.
 Default=

autoconf_config: Custom AutoConf config file for generating conformers and tautomers. These keywords are mutually exclusive: ['csrch', 'autoconf_config']
 Default=

prepare_input_structures: Preprocess input structures, converting coordinates from 2D to 3D and adding any missing hydrogens.
 Default=False