amorphous_nmr_driver.py Command Help

Command: $SCHRODINGER/run amorphous_nmr_gui_dir/amorphous_nmr_driver.py

usage: $SCHRODINGER/run amorphous_nmr_gui_dir/amorphous_nmr_driver.py
       [-h] [-property PROPERTY]
       [-keywords KEYWORD=VALUE KEYWORD=VALUE [KEYWORD=VALUE KEYWORD=VALUE ...]]
       [-small BASIS_SET] [-opt WHAT_TO_OPTIMIZE] [-distance DISTANCE]
       [-random RANDOM_SELECTIONS] [-molecules MOLECULE1,MOLECULE2...]
       [-use_charges PROPERTY] [-TPP THREADS] [-species_type MAESTRO_FILE]
       [-JOBNAME JOBNAME] [-HOST <hostname>]
       input_file

Given a structure with periodic boundary conditions, does the following for
each molecule in the structure: 1) Extract a cluster of the molecule and all
nearest neighbors, 2) Run a Jaguar NMR calculation. The NMR results are then
extracted into a .txt file. Copyright Schrodinger, LLC. All rights reserved.

positional arguments:
  input_file            Input file

options:
  -h, -help             Show this help message and exit.
  -property PROPERTY    The property to calculate. "nmr" computes NMR
                        shieldings, "tddft" computes TDDFT transition
                        energies, and "tadf" computes the S1-T1 energy gap
                        computed by TDDFT. (default: nmr)
  -keywords KEYWORD=VALUE KEYWORD=VALUE [KEYWORD=VALUE KEYWORD=VALUE ...], -k KEYWORD=VALUE KEYWORD=VALUE [KEYWORD=VALUE KEYWORD=VALUE ...]
                        Jaguar keyword to include in calculations. Can be
                        given multiple times, ex. -k iacc=1 -k gdftmed=-14. If
                        this is the last flag before the input/output file
                        names, use --to terminate the list of keywords.
                        (default: )
  -small BASIS_SET, -s BASIS_SET
                        Basis set to use for the neighboring molecules.
                        Default is 3-21G. (default: 3-21G)
  -opt WHAT_TO_OPTIMIZE, -o WHAT_TO_OPTIMIZE
                        Atoms whose position should be optimized. Choicesare
                        "none", "to_hydrogen" and "all". The default is
                        "none". Note that only bond lengths will be optimized,
                        and only atoms in the central molecule will be
                        optimized. This option is only available for NMR
                        calculations. (default: none)
  -distance DISTANCE, -d DISTANCE
                        When building a cluster for a molecule, include all
                        other molecules with any atoms within this many
                        Angstroms to the molecule in question. Default is 4.0.
                        (default: 4.0)
  -random RANDOM_SELECTIONS, -r RANDOM_SELECTIONS
                        Randomly choose this many molecules to run NMR
                        calculations for. The default is all molecules. See
                        also the -molecules flag. (default: None)
  -molecules MOLECULE1,MOLECULE2...
                        Run NMR calculations only for these molecules. The
                        value for this flag should be a comma-delimited list
                        of molecule numbers from the structure - do not use
                        spaces. The default is all molecules. See also the
                        -random flag. (default: None)
  -use_charges PROPERTY
                        Replace atoms in cluster neighbors with partial
                        charges. Atoms with the b_matsci_cluster_neighbor
                        property set to True will be replaced by their partial
                        charge in Jaguar calculations. The value given with
                        this flag is the atom property to use for partial
                        charges and should be in the r_x_property_name format.
                        Use the special value "esp" to indicate that ESP
                        charges should be computed using a B3LYP single point
                        and the basis set specified by -small. Charges will be
                        computed for a representative of each chemically
                        distinct neighboring molecule and those charges
                        applied to all neighbors of that species. (default:
                        None)
  -TPP THREADS          Number of threads to pass to jaguar run with the -TPP
                        flag. (default: 1)
  -species_type MAESTRO_FILE
                        If dimers should be restricted by molecule type, use
                        this flag to indicate the type of molecule that
                        -species_criteria applies to. The value passed with
                        this flag should be a Maestro (.mae, .maegz) file that
                        contains the structure of the species. This flag is
                        only used when -clusters is used. (default: None)
  -JOBNAME JOBNAME      Set jobname for this calculation. (default: None)

Job Control Options:
  -HOST <hostname>      Run job remotely on the indicated host entry.
                        (default: localhost)