csrch.py Command Help
Command: $SCHRODINGER/jaguar run csrch.py
usage: $SCHRODINGER/jaguar run csrch.py [-h] [-do_gas_csrch] [-max_conf <N>]
[-erg_window <X>]
[-erg_window_units <X>]
[-acc_level {high,quick,std}]
[-confsearch_method {mixed,lowmode,mcmm,confgen}]
[-add_extended_confs]
[-avoid_correct_lewis]
[-include_alternate_mesomers]
[-distinct_enantiomers]
[-disable_fallback_minimization]
[-constraints <N> [<N> ...]]
[-fixed_atoms <N> [<N> ...]]
[-cis_trans_constraint <N> [<N> ...]]
[-workflow_settings WORKFLOW_SETTINGS]
[-max_steps MAX_STEPS]
[-solvent {water,chcl3,octanol}]
[-forcefield FORCEFIELD]
[-renumber_atoms]
[-cluster_conformers]
[-num_clusters NUM_CLUSTERS]
[-cluster_asl CLUSTER_ASL] [-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>]
maefile
We take the name of a single .mae input file as an argument. The associated
CT is sent to MacroModel for a gas-phase or aqueous-phase (default)
conformational search and minimization, and the lowest-energy CT is then used
to create a new Jaguar input file.
positional arguments:
maefile
options:
-h, --help show this help message and exit
-do_gas_csrch Do gas-phase csrch instead of solution-phase.
-max_conf <N> Number of conformers to search for.
-erg_window <X> MacroModel energy window; default = 0.0 kj/mol
-erg_window_units <X>
MacroModel energy window units (kcal/mol or kJ/mol).
-acc_level {high,quick,std}
Accuracy level for conformational search; default = std
-confsearch_method {mixed,lowmode,mcmm,confgen}
Conformational search methodology; default = mixed
-add_extended_confs Run MacroModel a second time to add extended structures to the pool of conformers.
-avoid_correct_lewis Do not correct possible errors in Lewis structure in inputs. Note that Lewis correction may change charges.
-include_alternate_mesomers
If there are alternate reasonable mesomers of the input, use the union of the sets of rotatable bonds from all mesomers for conformerational search.
-distinct_enantiomers
Consider enantiomeric structures to be distinct.
-disable_fallback_minimization
If conformational search fails, do not fallback to a minimization unless the system has fewer than 3 unconstrained atoms
-constraints <N> [<N> ...]
Distance, angle, or dihedral constraint. Value of constraint is first, followed by atom indices. Fixed atoms should use the -fixed_atoms flag
-fixed_atoms <N> [<N> ...]
Atom indices to fix in place
-cis_trans_constraint <N> [<N> ...]
Torsion constraint which will reject conformers if violated (e.g. double bond stereochemistry). Give 4 atom indices followed by 0 if the that torsion should be cis and 90 if that torsion should be trans. General constraints should use -constraints flag, fixed atoms should use the -fixed_atoms flag
-workflow_settings WORKFLOW_SETTINGS
Workflow-specific settings
-max_steps MAX_STEPS Maximum conformational search steps. Overrides acc_level setting
-solvent {water,chcl3,octanol}
Solvent to use for conformational search; default = water
-forcefield FORCEFIELD
Forcefield to use in MacroModel. Default is OPLS4 if license found; otherwise OPLS_2005. Choices={'OPLS4', 'OPLS_2005'}
-renumber_atoms Renumber and rename atoms consistently for a set of conformers.
-cluster_conformers Instead of conformational search, cluster a given set of conformers by RMSD
-num_clusters NUM_CLUSTERS
Number of desired clusters to sort conformations into. If 0 (default) is specifed, the number of clusters is selected automatically
-cluster_asl CLUSTER_ASL
ASL expression to specify atoms over which RMSD is computed for clustering job. Default is 'all'
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.