autots Command Help
Command: $SCHRODINGER/autots
usage: $SCHRODINGER/jaguar run AutoTS.py [-h] [-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
Top-level script for AutoTS workflows
positional arguments:
infile Please specify one AutoTS .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.
-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.
AutoTS Input Keywords:
----------------------------------------
reactant: A list of full paths to Maestro structure files containing individual reactant molecules.
Default=[]
product: A list of full paths to Maestro structure files containing individual product molecules.
Default=[]
spectators: A list of paths to Maestro structure files containing individual spectator molecules.
Default=[]
refinish_dftname: Levels of theory to run refinement calculations with. Each specified will be run with each refine_basis.
Default=[]
refinish_basis: Basis sets to run refinement calculations with. Each specified will be run with each refinish_dftname.
Default=[]
alignment_atoms: The indices of the destination molecule's atoms considered most important for aligning graft molecules with the destination molecule.
Default=[]
sn2: Apply an atom numbering correction to SN2 reactions. This correction attempts to invert the chirality of the electrophilic center by renumbering terminal atoms.
Default=True
sn2_ignore_water: Ignore waters when determining atom numbering corrections for SN2 reactions.
Default=False
analytic_hessian: Compute an analytic Hessian when performing frequency analysis.
Default=True
optimize_inputs: If True, optimize initial complexes. This parameter will be automatically set to False if the parameters reactant_complex and product_complex are set and use_complex_inputs is True.
Default=True
optimize_outputs: If True the final (determined by IRC) minimum energy structures are optimized.
Default=True
exit_after_path: Exit job after constructing interpolated path.
Default=False
relax_path: Use the relaxed string method (RSM) to improve path.
Default=False
check_alignment_stability: If True, verify that alignment of reactant and product in complexformation is stable.
Default=True
form_rxn_complex: Optimally position the geometry of the reactant (entrance) and product (exit) complexes prior to path interpolation. If this is set to False the geometries will be the result of the initial geometry optimization. This parameter is automatically set to False if reactant_complex and product_complex are set and use_complex_inputs is set to True.
Default=True
use_complex_inputs: If the user has specified files for reactant_complex and product_complex, we will use those complexes rather than generate new ones in the workflow if this variable is set to True. Otherwise, the workflow will ignore those files and generate new complexes.
Default=False
recompute_input_lewis_structure: Recompute the Lewis structure of input structures for the purposes of renumbering complexes.
Default=False
localize_spectators: If True, localize spectator molecules near the reaction center. Otherwise, the entire input molecule will be considered for spectator interactions.
Default=True
qst_endpoints_are_min: Use minima instead of posed complexes as QST endpoints.
Default=False
skip_inf_sep: Do not perform calculations to compute the infinitely separated energy.
Default=False
free_energy: Compute the Gibbs free energy of infinitely separated complexes.
Default=False
use_template: Use a transition state template if one matches the input reaction type.
Default=True
debug_templates: Turn on extra printing for debugging template code.
Default=False
neglect_qst_displacement: Neglect displacement convergence criterion when optimizing the transition state guess.
Default=True
eliminate_multiple_frequencies: Employ techniques to remove multiple imaginary frequencies in transition state optimization.
Default=False
exit_on_unexpected_rxn: Exit the calculation if an unexpected chemical reaction occurs during the initial optimization. This indicates that the input structures are not stable at the requested level of theory.
Default=True
debug: Print extra debugging information.
Default=False
mm_opt_only: Use molecular mechanics (MM) to perform all geometry optimizations.
Default=False
mm_relax_path: Relax path by performing constrained optimizations with MM along interpolated path.
Default=False
relax_ts_guess: Relax TS guess with constrained optimization before TS optimization.
Default=True
use_unrelaxed_ts_on_failure: If relaxing the TS guess leads to a reaction or failure and this keyword is set to True, use the unrelaxed TS guess as is. Otherwise, a new TS guess method will be used.
Default=False
require_irc_success: If True we require the IRC to succeed before accepting a transition state.
Default=False
constrained_ts_search: Freeze the non-reacting part of the molecule when optimizing the transition state. This can enhance the success rate in large flexible systems.
Default=False
ts_vet_with_constraints: Project constraints out of Hessian when applying TS vetting. This setting only applies when constrained_ts_search=True. The alternative is to analyze the full Hessian which may contain eigenvectors corresponding to degrees of freedom that were not optimized.
Default=True
ts_guess_only: Exit job after constructing a transition state guess.
Default=False
use_default_templates: If keyword template_database_file is not set in the input file, use the user's default set of templates in the user resources directory.
Default=True
conf_search_gas_phase: If True, MacroModel conformational search will be performed in gas phase.
Default=False
conf_search_filter_reactive_optimizations: If True, remove any structures which undergo a chemical reaction when performing a Jaguar optimization during the conformational search workflow.
Default=True
use_mm_ts_guess: If True, guess a transition state by performing an MM constrained optimization using intermediate bond distances. These intermediate distances are defined by the keywords mm_ts_guess_b and mm_ts_guess_order.The transition state guess which is optimized is the highest energy point along a path passing through this point.
Default=False
optimize_raw_complexes: If True, optimize the initial complexes before computing path. Only for use with Hydrokinetic.
Default=False
generate_raw_path_only: If True, do not spline initially generated path
Default=False
conf_search: Perform a conformational search after locating transition states.
Default=False
conf_search_reactants: Perform a conformational search on reactant structures. Requires conf_search to also be set to True.
Default=True
conf_search_products: Perform a conformational search on product structures. Requires conf_search to also be set to True.
Default=True
conf_search_intermediates: Perform a conformational search on intermediate structures. Requires conf_search to also be set to True.
Default=True
conf_search_ts: Perform conformational search on transition state structures. Requires conf_search to also be set to True.
Default=True
syn_renumbering: Determines whether or not syn renumbering is performed.
Default=True
final_minimize_path: Determines whether or not product/reactant realignment is run. Principally for testing atom numbering.
Default=True
accept_secondary_afir_path: Determines whether or not an afir path is accepted if a secondary reaction has occured.
Default=True
afir_minima_to_minima: Determines whether or not an afir path from minima to minima is done if all methods have failed.
Default=False
store_autots_data: Determines whether or not to send data to a server at the end of the job. Only applicable if AutoTS server hostname and port are given
Default=True
invert_reactive_stereocenters: Generate an alternate stereochemical outcome of a stereogenic reaction after locating transition states by inverting the chirality in the reaction center, leaving all other chiral centers uninverted.
Default=False
ignore_chirality_mismatch: Ignore errors in chirality (mismatches) outside of the reaction center.If False, AutoTS will exit if chirality mismatches are found.
Default=False
repair_ts_guess_stereochem: If the TS guess was found to be likely to lead to incorrect stereoisomeric reactants/products, we can try and correct the guess automatically. If True, AutoTS will attempt to repair the guess.
Default=True
die_on_bad_ts_guess_stereochem: If the TS guess was found to be likely to lead to incorrect stereoisomeric reactants/products and we were unable to automatically repair the guess, should the calculation proceed. If True, AutoTS will exit if the TS guess could not be repaired.
Default=False
fixed_ts_stereochemistry_label: If True, all chiral centers that only occur in the TS are ensured to be labeled R when all active bonds are formed.
Default=False
flexible_metal_coordination: If True, ignore the bonding of metals in the system. Used when only the chemistry of an organic fragment is of interest and coodination of the metal is not.
Default=False
conf_search_metal_centers: If False, freeze bond angles where the central atom is a metal.
Default=True
conf_search_cluster_conformers: Choose conformers for QM optimization from different clusters. This setting attempts to diversify the conformers optimized by the QM method by choosing low energy conformers out of different clusters, grouped by cartesian rmsd, requires a Canvas License.
Default=False
water_wire: Analyze inputs and attempt to label to encourage water wire formation
Default=False
allow_disjoint_water_wire: Adjust automatic water wire formation analysis to allow water wires that may be disjoint
Default=False
multiplicity: Overall spin multiplicity of reaction complex.
Default=1
charge: Overall charge of reaction complex.
Default=0
max_n_active_bonds: The maximum number of active bonds to consider in a reaction. If a job fails because it could not find a valid active bond set, increasing this may help but the job runtime will be substantially increased.
Default=5
afir_min_fc: Minimum force constant for AFIR paths.
Default=40
path_npts: Number of points to initially sample the reaction path (before interpolation).
Default=31
max_connections: Maximum number of connections to search for.
Default=10
template_order: Order of the subset of atoms used to make constraints on template based transition state guess. Order 1 uses only reaction center atoms. Order 2 uses the reaction center plus nearest neighbors, etc.
Default=1
conf_search_max_qm_conformers: Maximum number of conformers to re-optimize with QM level of theory.
Default=10
conf_search_max_mm_conformers: Maximum number of conformers to request from an initial MM based conformational search.
Default=200
constrained_ts_search_order: Defines the size of the active region when constrained_ts_search=True. The active region is the reaction center plus (order-1)th neighbors. Meaningful values are positive integers.
Default=3
pts_guess_with_ts: The number of points around each maximum energy point along the interpolated reaction path used as a transition state guess. If 0, only one point (the maximum energy) is considered. Concretely, if there are n maximum points along the path, then in total n*pts_guess_with_ts of points will be optimized if pts_guess_with is odd, and n*pts_guess_with_ts + 1 of points will be returned if pts_guess_with_ts is even. This setting will cause several TS optimizations to be run in parallel.
Default=0
conf_search_numb_clusters: Number of conformational clusters requested if a value of zero is requested then the number of clusters is determined automatically. See also keyword conf_search_cluster_conformers.
Default=0
conf_search_conf_per_clusters: Number of conformations to take from each conformational cluster. See also keyword conf_search_cluster_conformers.
Default=1
autots_server_port: port number for AutoTS server
Default=0
loose_opt_scaling: Scaling factor for convergence criterion when doing loose optimization. This includes AFIR path construction, initial optimization of reaction complexes and constrained optimization to prepare transition state guess geometries.
Default=3.0
conf_search_loose_opt_scaling: Scaling factor for convergence criterion when doing loose optimization during conformational search stage. This includes constrained optimization used to prepare transition state guess geometries.
Default=10.0
vdw_scale: Scales the vdw radii used to position individual molecules when making complexes.
Default=1.0
path_dx: RMS difference between two structures along the interpolated path. Increasing this value will increase the number of points along the path.
Default=0.2
rms_thresh: Threshold for RMSD between two structures considered to be different.
Default=0.25
irc_rms_thresh: RMS threshold for sanity check on IRC. This check ensures that the IRC endpoints moved sufficiently far away from the transition state.
Default=0.02
ts_vet_max_freq: Maximum frequency (in cm-1) to consider when vetting transition vectors of an optimized transition state. For example, if this parametert is set to -20.0 only vibrational modes with frequencies less than this value will be considered as possible transition vectors. Note that this setting is independent of the requirement that there is only one negative eigenvalue of the Hessian, this latter requirement is controlled by the setting ts_acceptance_strictness.
Default=0.0
conf_search_energy_window: Energy window (kcal/mol) used in conformational search. Only conformers with energies within this value of the minimum energy conformer are kept.
Default=10.0
conf_search_qm_energy_window: Energy window (kcal/mol) used in conformational search. Only conformers with energies within this value of the minimum energy conformer are kept after constrained optimization of transition state (TS) geometries and before TS optimization
Default=10.0
bond_stretch_fraction: Percent change allowed in a stretching bond before it is considered broken when determining if two structure are conformers.
Default=0.5
mm_ts_guess_b: Value of the parameter b used to compute a guessed TS bond length = b/((b-1)*o + 1), where o is the bond order. The bond order is controled by the parameter mm_ts_guess_order.
Default=2.0
mm_ts_guess_order: Value of bond order (o) used to compute guess TS bond length = b/((b-1)*o + 1). The parameter b is controlled by mm_ts_guess_b.
Default=0.5
conf_search_boltzmann_thresh: Threshold on Boltzmann factor used to filter high energy structures prior to frequency evaluation.
Default=0.005
frozen_atoms_rmsd_thresh: Threshold for ensuring that frozen atoms are initially aligned
Default=0.3
reactant_complex: Full path to a Maestro structure file containing the reactant (entrance) complex. If this is defined the initial optimization and positioning of the reaction complexes will be skipped.
Default=
product_complex: Full path to a Maestro structure file containing the product (exit) complex. If this is defined the initial optimization and positioning of the reaction complexes will be skipped.
Default=
complex_formation: Methodology used to position molecules and orient torsion angles of rotatable bonds in reactant and product complexes.
Default=distance-minimization
spectator_esp: Methodology used to position spectator molecules in reactant and product complexes.
Default=jaguar
interpolation: Coordinate type used to perform reaction path interpolation.
Default=distance
template_database_file: Path to a Maestro structure file containing transition state templates. This file should be prepared by the utility store_reaction_template.
Default=
full_path_file: Full path mae file produced by a previous, succesful AutoTS job. To be used with jobtype=energy_correction, jobtype=refinish_only, or jobtype=conf_search.
Default=
full_path_separated: Separated full path mae file produced by a previous, succesful AutoTS job. To be used with jobtype=energy_correction, jobtype=refinish_only, or jobtype=conf_search.
Default=
conf_search_file: Conformation search mae file produced by a previous, succesful AutoTS job run with conf_search enabled. To be used with jobtype=energy_correction, conf_search or refinish_only.
Default=
units: Units used for printing summary tables.
Default=kcal/mol
comparison_type: Method used to determine if two structures are different.
Default=conformers_only
irc_type: Methods used to perform IRC.
Default=lqa_irc
irc_path_type: Type of path computed by IRC (IRC or MEP)
Default=mep
jobtype: Specifies the workflow.
Default=full
ts_acceptance_strictness: Strictness for verification of a candidate transition state.
Default=std
ts_vetting_type: Methodology used when verifying a candidate transition state.
Default=both
conf_search_ts_vetting_type: Methodology used when verifying a candidate transition state in the conformational search stage.
Default=distance
conf_search_constraint_type: Type of constraint to be used when performing MacroModel based conformational search on transition state geometries
Default=fixed-atoms
initial_hessian_type: Type of guess hessian used in transition state optimization.
Default=refine
ts_search_type: Algorithm used to perform transition state optimizations.
Default=eigenfollow
follow_eigenvector: Method to choose which eigenvector to follow in a transition state optimization step.
Default=active
conf_search_mode: Conformational search can either be applied to reaction complexes or separated molecules.
Default=separated
conf_search_accuracy_level: MacroModel conformational search accuracy level. Acceptable values are 0 (low accuracy) and 1 (high accuracy).
Default=high
irc_ts_vetting_type: Defines how the results of an IRC are used when verifying a candidate transition state. Only applied if require_irc_success=True.
Default=reaction_occurred
path_type: Selects a method to compute a reaction path from reactants to products.
Default=afir
autots_server_hostname: hostname for AutoTS server
Default=
refinish_mode: Selects what type of refinish calculations should be done when refinish_dftname or refinish_basis are set. If a frequency calculation is requested then a geometry optimization will be carried out first.
Default=none
graft_structures: Path to a .mae file containing structures that should be grafted into the reaction.
Default=
destination_molecule: The structure title denoting which molecule should be taken as the destination when grafting
Default=
graft_refinement: The level of theory for to apply when refining raw graftedreaction complexes before calculating QM energy.
Default=forcefield
prepare_input_structures: Preprocess input structures, converting coordinates from 2D to 3D and adding any missing hydrogens.
Default=False