esol.py Command Help
Command: $SCHRODINGER/jaguar run esol.py
usage: $SCHRODINGER/jaguar run esol.py [-h] [-WAIT] [-DEBUG] [-jobname <name>]
[-subdir] [-recover] [-no_subjob_files]
[-scr <absolute path>] [-PARALLEL <N>]
[-max_threads <T>]
[-procs_per_node <N>]
[-gpu_host <host>:<M>]
[-use_one_node | -use_multiple_nodes]
[-HOST <host>:<M>]
[-SUBHOST <host>:<M>] [-SAVE]
[-NOJOBID] [-OPLSDIR <oplsdir>]
[-MLFF_DATA <mlff_data_dir>]
infile
Top-level script for E-Sol workflow
positional arguments:
infile Please specify one Esol .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.
-gpu_host <host>:<M> Host on which to run Jaguar subjobs that request GPU. The optional :<M> defines the maximum number of simultaneous GPU subjobs. Defaults to the value resolved from -SUBHOST/-HOST. Validated only when a GPU subjob is actually launched.
-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.
-MLFF_DATA <mlff_data_dir>
Enable custom MLFF models from specified directory for workflows which support it.
Esol Input Keywords:
----------------------------------------
input: Path (absolute or relative) to a file (.mae/.maegz/.sdf/.sdfgz) containing molecular structures.
Default=
protocol: Select a protocol for the E-Sol calculation.
`default`: Default settings.
The `mlff_<stage>` protocols use MLFF up through the named stage and QM for any later stages:
`mlff_filter`: MLFF conformer filtering, then QM geopt and single-point.
`mlff_geopt`: MLFF conformer filtering and geopt, then QM single-point.
`mlff_energy`: MLFF for all stages.
`full_exhaustive_dft`: QM for all stages with exhaustive conformer search.
Individual keywords override the protocol settings when both are specified.
Default=default
conf_search_phases: Phase(s) to run conformer search in. Only used when `conf_search_program=macromodel`.
Default=['gas', 'water']
conf_search_program: Program to use for conformer search. Options are "macromodel" or "prime".
"prime" search is only applicable for systems containing macrocycles (rings with 10 or more atoms).
Default=macromodel
use_input_state_penalties: Skip the Epik run and use the existing Epik state penalty
for totally neutral structures (no formal charges) with the `r_epik_State_Penalty` property.
Default=False
geopt_functional: Functional to use during QM geopt stage
Default=B3LYP
geopt_basis: Basis to use during QM geopt stage
Default=LACVP*
geopt_solvation: Solvation method to use during QM geopt stage
Default=NONE
sp_functional: Functional to use during QM single-point stage
Default=M06-2X
sp_basis: Basis to use during QM single-point stage
Default=LACVP**
sp_solvation: Solvation method to use during QM single-point stage
Default=PBF
conf_sets_provided: If set, groups the molecules in "input" into sets of conformers and skips conformer search.
Default=False
mlff_auto_fallback: Controls fallback behavior when QRNN/MLFF cannot be used, either because individual molecules are unsupported or because a license is unavailable.
Only applies if QRNN/MLFF is requested for a QM stage of E-Sol.
`NONE`: Molecules that cannot use QRNN/MLFF are written to a separate .mae file.
`QM`: Molecules that cannot use QRNN/MLFF fall back to default QM settings.
`XTB`: Molecules that cannot use QRNN/MLFF fall back to xTB (default).
When a license is unavailable, the fallback applies to all input molecules and is resolved during input validation.
Default=XTB
conf_filter: Use MLFF geopts to filter conformers obtained from
Macromodel conformer search. Multiplies the Macromodel energy
threshold (5 kcal/mol) and "n_conformers_conf_search"
values by "conf_filter_factor" and then uses MLFF energies to filter
the conformers with respect to "conf_energy_window". A maximum of
"n_conformers_to_score" conformers will pass the filter. If molecules
are unsupported by QRNN/MLFF, fall back to xTB conformer filtering
protocol. QRNN/MLFF require a forcefield license. Available options are:
['QRNN', 'MLFF', 'XTB', 'NONE'].
Default=NONE
n_conformers_conf_search: Maximum number of conformers to keep from each conformer search.
Default=12
n_conformers_to_score: Maximum number of conformers to score with QM.
Default=12
conf_filter_factor: Factor by which to loosen energy threshold and n_conformers_conf_search for Macromodel conformer search job if QRNN/MLFF conformational filtering stage has been requested.
Should be a positive number.
Default=1.5
conf_energy_window: Window to filter high-energy structures at end of QRNN/MLFF conformational filtering stage.
Should be a positive number.
Default=5.0
prepare_input_structures: Preprocess input structures, converting coordinates from 2D to 3D and adding any missing hydrogens.
Default=False