materials_conformational_search_driver.py Command Help
Command: $SCHRODINGER/run materials_conformational_search_gui_dir/materials_conformational_search_driver.py
usage: $SCHRODINGER/run materials_conformational_search_gui_dir/materials_conformational_search_driver.py
[-h] -mae_files <molecule_1>.mae <molecule_2>.mae ...
[<molecule_1>.mae <molecule_2>.mae ... ...]
[-csearch_engine {Macromodel,Crest}] [-forcefield FORCE_FIELD]
[-skip_eta_rotamers] [-metal_index METAL_INDEX] [-com_fn COM_FN]
[-seed SEED] [-n_conformers N_CONFORMERS]
[-pp_rel_energy_thresh PP_REL_ENERGY_THRESH] [-return_csearch_files]
[-qm_selection] [-n_rotamers N_ROTAMERS] [-jaguar]
[-jaguar_keywords [<key_1>=<value_1> [<key_2>=<value_2> ...]]] [-mopac]
[-method METHOD] [-max_i_freq WAVENUMBERS] [-descriptors]
[-skip_boltz_avg] [-dedup_geom_eps DEDUP_GEOM_EPS] [-TPP TPP]
[-HOST <hostname>] [-SAVE] [-JOBNAME JOBNAME]
Driver for conformational search for molecular materials. Copyright
Schrodinger, LLC. All rights reserved.
options:
-h, -help Show this help message and exit.
-mae_files <molecule_1>.mae <molecule_2>.mae ... [<molecule_1>.mae <molecule_2>.mae ... ...]
Specify Maestro input files. Each unique molecule
should have its own file but each file may contain
multiple conformations of the target molecule. These
conformations will seed a MacroModel conformational
search. Files should be space-delimited. (default:
None)
-csearch_engine {Macromodel,Crest}
The engine to use for the conformational search.
(default: Macromodel)
-forcefield FORCE_FIELD
Force field to use. Valid force fields are OPLS_2005
and S-OPLS (default: S-OPLS)
-skip_eta_rotamers Specify that eta rotamers generation will be skipped.
(default: False)
-metal_index METAL_INDEX
Index of the metal atom around which to generate eta-
rotamers. If not provided and the structure has a
single metal atom then that index will automatically
be used. (default: None)
-com_fn COM_FN Use the settings in this example MacroModel .com file
for the conformational search rather than the default
settings. (default: None)
-seed SEED Specify a seed for the random number generator used
for any conformational searches. (default: 1234)
-n_conformers N_CONFORMERS
Specify the number of conformers to search for.
(default: 5)
-pp_rel_energy_thresh PP_REL_ENERGY_THRESH
If given, specifies to instead search for all
conformers with relative energies <= this value in
kJ/mol. (default: None)
-return_csearch_files
Use this option to return all output files from any
conformational search subjobs. (default: False)
-qm_selection Use this option to select conformers from quantum
energies rather than from classical energies.
(default: False)
-n_rotamers N_ROTAMERS
Specifies the number of guess rotamers for eta-bound
ligands prior to MacroModel conformational search. If
not given then it will be twice the number of ring
atoms in the haptic ring. (default: None)
-jaguar Use this option to run Jaguar geometry optimizations
and frequencies on each of the determined conformers.
(default: False)
-jaguar_keywords [<key_1>=<value_1> [<key_2>=<value_2> ...]]
Specify Jaguar &gen section key-value pairs. Each key-
value pair should be separated from the next by
whitespace and each should be represented in terms of
a "<key>=<value>" pair. (default: ['dftname=B3LYP',
'basis=LACVP**'])
-mopac Use this option to run Mopac geometry optimizations
and frequencies on each of the determined conformers.
(default: False)
-method METHOD Specify the Mopac method. (default: PM6)
-max_i_freq WAVENUMBERS
Check the number of imaginary frequencies using this
tolerance in wavenumbers (cm^-1). (default: 0)
-descriptors Use this option to report cheminformatics descriptors
for all conformers. (default: False)
-skip_boltz_avg By default cheminformatics descriptors are Boltzmann
averaged over conformers and a single conformer
provided as output. Use this option to skip the
Boltzmann averaging and provide all conformers as
output. (default: False)
-dedup_geom_eps DEDUP_GEOM_EPS
Reduce the number of calculations by deduplicating the
input structures based on geometry, using this
threshold in Ang., and only calculating the
representatives. A value of zero means no
deduplicating. (default: 0.25)
-TPP TPP Specify the number of threads to use for parallelizing
any Jaguar subjobs. (default: 1)
Job Control Options:
-HOST <hostname> Run job remotely on the indicated host entry.
(default: localhost)
-SAVE Return zip archive of job directory at job completion.
(default: False)
-JOBNAME JOBNAME Provide an explicit name for the job. (default: None)