spectroscopy.py Command Help
Command: $SCHRODINGER/jaguar run spectroscopy.py
usage: $SCHRODINGER/jaguar run spectroscopy.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 Jaguar Spectroscopy (spectroscopy.py).
Given an input structure, the workflow will:
(1) Generate full space of conformers using Macromodel
(2) Refine conformers using DFT and/or MLFF methods
(3) Calculate Boltzmann-averaged spectra and properties
Currently, IR/UV-Vis/VCD/ECD, NMR and Optical Rotation spectroscopies are supported.
An example input file, for a VCD calculation using default level of theory,
is shown below:
infile = molecule.mae
vcd = True
&JaguarKeywords
&
positional arguments:
infile Single spectroscopy input 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.
Jaguar Spectroscopy Input Keywords:
----------------------------------------
infile: Input .mae file containing either one structure or a set of conformers. If it contains conformers, conformer search and atropisomer generation are skipped.
Default=
temperature: Temperature at which to calculate thermodynamic quantities used in computing Boltzmann weights.
This takes precedence over specifying `tmpini` in the &JaguarKeywords section.
Default=298.15
solvent: Solvent to use in all calculations
Default=None
skip_csearch: Skip conformational search
Default=False
skip_crefine: Skip conformational refinement (QM Geometry Optimization) and thus redundant conformer elimination via QM energy
Default=False
skip_celim: Skip redundant conformer elimination via max atom deviation
Default=False
forcefield: Forcefield to use in conformational search. Default is OPLS4 if license found; otherwise OPLS_2005.
Choices = {'OPLS_2005', 'OPLS4'}
Default=OPLS4
conf_search_method: Conformational search method used by Macromodel to generate conformers.
Available options:
- mcmm: global PES searching via the Monte Carlo Multiple Minimum (MCMM) method
- lowmode: local PES searching via the Low-Mode Conformational Search (LMCS) method
- mixed: hybrid MCMM/LMCS method
- confgen: fast conformational search for ligands via Macromodel's ConfGen technology
See Macromodel documentation for further references.
Choices = {'mixed', 'mcmm', 'lowmode', 'confgen'}
Default=mixed
conf_search_steps: Number of conformational search steps. If set, overrides number of steps as set by `conf_search_acc`.
Default=None
conf_search_acc: Accuracy level of MacroModel's conformer search. It sets the number of conformational search steps.
Available options:
- quick: 100 steps
- std: 1000 steps
- high: 3000 steps
Choices = {'std', 'high', 'quick'}
Default=std
mm_energy_window: Energy window (kcal/mol) for retaining conformers from conf. search
Default=5.0
outconfs: Maximum number of conformers to retain
Default=100
max_atom_dev: Maximum allowed atom deviation in conf. elimination
Default=0.5
qm_energy_window: QM energy window (kcal/mol) for retaining structures for CD/NMR calculations
Default=5.0
mlff_conf_energy: Use energies from the model specified by `mlff_method` to order conformers generated by Macromodel.
Replaces the deprecated `nn_conf_energy` option.
Default=False
mlff_geopt: Use the model specified by `mlff_method` for conformer refinement.
Replaces the deprecated `nn_geopt` option.
Default=False
mlff_method: Method to use for conformer refinement if `mlff_geopt` or `mlff_conf_energy` is set.
Choices = {'mlff', 'qrnn'}
Default=qrnn
final_dft_geopt: Ensures final step of conformer refinement is geometry optimization at the DFT level.
Since this is the default behavior, this option only affects runs using `mlff_geopt`
Default=False
ir: Calculate IR spectra.
Default=False
uv_vis: Calculate UV-Vis spectra.
Default=False
vcd: Calculate VCD spectra. Note that an IR spectrum is generated as part of the VCD calculation.
Default=False
ecd: Calculate ECD spectra. Note that a UV-Vis spectrum is generated as part of the ECD calculation.
Default=False
spectra_nm_interval: Interval between x-axis points in generated csv files of spectra with x-axis units of nm (UV-Vis/ECD).
If <= 0, csv files will have constant energy intervals (10 cm-1) instead of constant nm intervals.
Default=0.1
ecd_skip_thermo: Applies to jobs that calculate only ECD.
Skips explicit calculation of free energies and uses electronic energies of final set of conformers instead.
Default=False
nmr: Calculate NMR chemical shifts, spin-spin couplings, and H-H/H-F vector distances for NOE analysis.
Equivalent to setting all three of the nmr properties: `chem_shifts`, `ssc`, and `noe`.
Default=False
chem_shifts: Calculate NMR chemical shifts. Has no additional effect if `nmr` is also set.
Default=False
ssc: Calculate spin-spin couplings. Has no additional effect if `nmr` is also set.
Default=False
noe: Calculate H-H and H-F vector distances for NOE analysis.
This option allows one to skip costly NMR calculations if used in the absence of `nmr`/`ssc`/`chem_shifts`.
Note that vector distances are also computed when any of the above-mentioned options are set.
Default=False
only_average_nmr: Skip calculation of individual conformer spectra, just compute Boltzmann averaged NMR spectrum.
Default=False
nmr_field: Strength of NMR magnetic field in 1H frequency (MHz) for spectrum simulation.
Default=500.0
coupling_threshold: The threshold (in Hz) below which J-couplings will be omitted from the spectrum simulation as their effects are below the resolution of most spectrometers.
Lowering this may give additional splitting detail for conjugated systems at the cost of *significantly* increased runtime and memory use.
Note that smaller couplings may still be pruned during subgraph generation if their inclusion would make the calculation intractable, see `max_subgraph_size`.
Default=1.0
max_subgraph_size: Maximum allowable size for subgraphs to control memory explosion in NMR spectrum simulations.
In the worst case memory requirements grow as ~ O[N*4^N] with this parameter. Any subgraphs generated that have more spins than this (default 14) will have their smallest magnitude couplings (edges) iteratively pruned until they are manageable.
Default=14
nmr_resolution_ppm: The resolution in ppm of the NMR spectrum. It automatically sets the number of points used in the NMR spectrum simulation.
Default=0.002
nmr_types: The types of NMR experiment to simulate. Adding this option without specify any types will disable spectrum simulation.
Choices = ['11B', '31P', '19F', '13C', '15N', '1H']
Default=['11B', '31P', '19F', '13C', '15N', '1H']
nmr_distinct_nuclei: Index of atom(s) to consider as NMR inequivalent when performing chemical shifts and spin-spin couplings averaging. Atoms not in this list will be automatically checked for NMR equivalence and averaged accordingly.
Default=[]
compute_all_ssc: If set, compute spin-spin couplings for all pair of atoms. Default is to only compute relevant spin-spin couplings for the requested type of NMR spectra.
Default=False
peak_height_factor: Scale factor used to automatically set minimum height for identifying peaks in the theoretical NMR spectrum. E.g.: 0.01 = one percent of maximum signal height.
Note that this value has no effect in the NMR spectrum simulation; only affects the spectrum post-processing.
Default=0.02
optrot: Calculate optical rotation (ORD).
Default=False
experimental: Path to a file containing experimental NMR data. This can be either:
a) CSV file containing (ppm, intensity) experimental NMR spectrum data.
b) A text file containing an NMR spectrum blurb in ACS format
https://pubsapp.acs.org/paragonplus/submission/acs_nmr_guidelines.pdf
Default=
ignore_protons_for_assignment: Atom names from that should be ignored when matching theoretical NMR spectra to an experimental spectrum.
Default=[]
n_trials: Number of trials that should be run when performing a Monte Carlo search because linear sum assignment has failed. More trials increase search coverage.
Default=1000
mc_search_temperature: The temperature (arbitrary units) for the Monte Carlo search if linear sum assignment fails. Must be a positive non-zero integer. Temperature scale depends on how closely the theoretical and experimental spectra match. Too low temperature and we may miss good combinations, too high and search will be essentially random.
Default=0.5
exclude_regions: Regions of the experimental spectrum to ignore as a comma separated list of start:stop pairs, e.g. -0.1:0.1,0.5:0.75
Default=[]
keep_zero_ppm_peak: Flag that peaks in the experimental spectrum between 0.1 ppm and -0.1 ppm should not be considerd the TMS reference peak.
Default=False
threshold: The scale factor used to automatically determine thresholding value for identifying peaks in the experimental spectrum. e.g. 0.03 sets the threshold at 3% between signal minimum and maximum.
Default=0.03
discrimination: When parsing the experimental spectrum this controls how large a gap of low signal is required to consider further different peaks as separate proton signals. Too low will result in split peaks being incorrectly broken apart. Too high and assignment detail may be lost.
Default=0.025
check_for_atropisomers: Account for atropisomers. Can automatically try to determine the relevant dihedral, or one can specify a dihedral to inspect via `target_dihedral`.
Currently only supports atropisomerism consisting of two atropisomers around one dihedral.
Default=False
target_dihedral: Dihedral to inspect for atropisomerism. Passed in as list of atom indices or atom names, e.g. `[3,6,5,7]` or `[C3,C6,N5,C7]`. Only has an effect if `check_for_atropisomers` is also set.
Default=None
pes_method: Method used to optimize rotamers to fit the rotational PES. If not set, uses QRNN/xTB. May set to any valid DFT functional.
Default=None
pes_basis: Basis set to use if `pes_method` is a DFT functional.
Default=6-31G**
prepare_input_structures: Preprocess input structures, converting coordinates from 2D to 3D and adding any missing hydrogens.
Default=False