spectroscopy.py Command Help
Command: $SCHRODINGER/jaguar run spectroscopy.py
usage: $SCHRODINGER/jaguar run spectroscopy.py [-h] [-ir] [-vcd] [-uv_vis]
[-ecd] [-optrot]
[-spectra_nm_interval SPECTRA_NM_INTERVAL]
[-ecd_skip_thermo] [-nmr]
[-chem_shifts] [-ssc] [-noe]
[-nmr_field NMR_FIELD]
[-coupling_threshold COUPLING_THRESHOLD]
[-max_subgraph_size MAX_SUBGRAPH_SIZE]
[-nmr_resolution_ppm NMR_RESOLUTION_PPM]
[-nmr_types [{31P,13C,15N,1H,11B,19F} ...]]
[-nmr_distinct_nuclei NMR_DISTINCT_NUCLEI [NMR_DISTINCT_NUCLEI ...]]
[-compute_all_ssc]
[-peak_height_factor PEAK_HEIGHT_FACTOR]
[-experimental EXPERIMENTAL]
[-ignore_protons_for_assignment IGNORE_PROTONS_FOR_ASSIGNMENT [IGNORE_PROTONS_FOR_ASSIGNMENT ...]]
[-n_trials N_TRIALS]
[-mc_search_temperature MC_SEARCH_TEMPERATURE]
[-exclude_regions EXCLUDE_REGIONS]
[-keep_zero_ppm_peak]
[-threshold THRESHOLD]
[-discrimination DISCRIMINATION]
[-skip_csearch] [-skip_crefine]
[-skip_celim]
[-outconfs OUTCONFS]
[-forcefield FORCEFIELD]
[-conf_search_method CONF_SEARCH_METHOD]
[-conf_search_steps CONF_SEARCH_STEPS]
[-conf_search_acc {high,quick,std}]
[-mm_energy_window MM_ENERGY_WINDOW]
[-qm_energy_window QM_ENERGY_WINDOW]
[-max_atom_dev MAX_ATOM_DEV]
[-mlff_conf_energy]
[-mlff_geopt]
[-mlff_method {qrnn,mlff}]
[-final_dft_geopt]
[-check_for_atropisomers]
[-target_dihedral TARGET_DIHEDRAL]
[-pes_method PES_METHOD]
[-pes_basis PES_BASIS]
[-solvent SOLVENT]
[-temperature TEMPERATURE]
[-only_average_nmr] [-k QMKEYS]
[-skip_3d_conversion] [-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
High-level script for calculating Boltzmann-averaged spectra
and properties with Jaguar. Currently, supports IR/UV-Vis/VCD/ECD/NMR.
positional arguments:
infile Please specify a single .mae file. If it contains multiple structures, conformer search is skipped.
options:
-h, --help show this help message and exit
-solvent SOLVENT Solvent to use in all calculations
-temperature TEMPERATURE
Temperature at which to calculate thermodynamic quantities used in computing Boltzmann weights. This takes precedence over passing tmpini to -keyword option
-only_average_nmr Skip calculation of individual conformer spectra, just compute Boltzmann averaged NMR spectrum.
-k QMKEYS, -keyword QMKEYS, --keyword QMKEYS
keyword=value setting for all QM calculations (conf. refinement, free energy, and spectrum calculations)
-skip_3d_conversion Do not preprocess input structures to convert from H-less or 2D structures to full 3D structures.
Other Spectroscopies:
Note that -ir/-vcd/-uv_vis/-ecd cannot be set in conjunction with options in "NMR Spectroscopy" (-nmr/-ssc/-chem_shifts/-noe)
-ir Calculate IR spectra.
-vcd Calculate VCD spectra. Note that an IR spectrum is generated as part of the VCD calculation.
-uv_vis Calculate UV-Vis spectra.
-ecd Calculate ECD spectra. Note that a UV-Vis spectrum is generated as part of the ECD calculation.
-optrot Calculate optical rotation (ORD).
-spectra_nm_interval 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.
NMR Spectroscopy:
Note that -nmr/-chem_shifts/-ssc/-noe cannot be set in conjunction with some options in "Other Spectroscopies" (-ir/-vcd/-uv_vis/-ecd)
-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.
-chem_shifts Calculate NMR chemical shifts. Has no additional effect if -nmr is also set.
-ssc Calculate spin-spin couplings. Has no additional effect if -nmr is also set.
-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 -nmr/-ssc/-chem_shifts options are set.
-nmr_field NMR_FIELD Strength of NMR magnetic field in 1H frequency (MHz) for spectrum simulation.
-coupling_threshold 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.
-max_subgraph_size MAX_SUBGRAPH_SIZE
Maximum allowable size for subgraphs to control memory explosion in NMR spectrum sim. 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.
-nmr_resolution_ppm NMR_RESOLUTION_PPM
The resolution in ppm of the NMR spectrum. It automatically sets the number of points used in the NMR spectrum simulation.
-nmr_types [{31P,13C,15N,1H,11B,19F} ...]
The types of NMR experiment to simulate. Adding this option without specify any types will disable spectrum simulation.
-nmr_distinct_nuclei NMR_DISTINCT_NUCLEI [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.
-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.
-peak_height_factor 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.
NMR Spectroscopy Assignment:
Further options controlling how NMR simulation is used to assign protons to peaks in a provided experimental NMR spectrum.
-experimental 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
-ignore_protons_for_assignment IGNORE_PROTONS_FOR_ASSIGNMENT [IGNORE_PROTONS_FOR_ASSIGNMENT ...]
Atom names from that should be ignored when matching theoretical NMR spectra to an experimental spectrum.
-n_trials 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.
-mc_search_temperature 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.
-exclude_regions 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
-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.
-threshold 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.
-discrimination 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.
Conformer Generation Options:
-skip_csearch Skip conformational search
-skip_crefine Skip conformational refinement (QM Geometry Optimization) and thus redundant conformer elimination via -qm_energy_window
-skip_celim Skip redundant conformer elimination via max atom deviation
-outconfs OUTCONFS Maximum number of conformers to retain
-forcefield FORCEFIELD
Forcefield to use in conformational search. Default is OPLS4 if license found; otherwise OPLS_2005. Choices = {'OPLS4', 'OPLS_2005'}
-conf_search_method CONF_SEARCH_METHOD
Conformational search method
-conf_search_steps CONF_SEARCH_STEPS
Number of conformational search steps. If set,
overrides number of steps as set by -conf_search_acc (Quick=100, Standard=1000, Thorough=3000).
-conf_search_acc {high,quick,std}
Accuracy level of MacroModel's conformer search; defaults to 'std'.
-mm_energy_window MM_ENERGY_WINDOW
Energy window (kcal/mol) for retaining conformers from conf search
-qm_energy_window QM_ENERGY_WINDOW
Energy window (kcal/mol) for retaining structures for CD calculations
-max_atom_dev MAX_ATOM_DEV
Maximum allowed atom deviation in conf. elimination
-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.
-mlff_geopt Use the model specified by `mlff_method` for conformer refinement. Replaces the deprecated `-nn_geopt` option.
-mlff_method {qrnn,mlff}
Method to use for conformer refinement if `mlff_geopt` or `mlff_conf_energy` is set.
-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
Atropisomerism Options:
Options controlling if workflow checks for atropisomerism of input compounds
-check_for_atropisomers
Account for atropisomers. Can automatically try to determine the relevant dihedral, or one can pass in a dihedral to inspect via '-target_dihedral'. Currently only supports atropisomerism consisting of two atropisomers around one dihedral.
-target_dihedral 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.
-pes_method 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.
-pes_basis PES_BASIS Basis set to use if 'pes_method' is a DFT functional. Defaults to 6-31G**
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.