bond_dissociation_driver.py Command Help
Command: $SCHRODINGER/run bond_dissociation_gui_dir/bond_dissociation_driver.py
usage: $SCHRODINGER/run bond_dissociation_gui_dir/bond_dissociation_driver.py
[-h]
[-keywords KEYWORD=VALUE KEYWORD=VALUE [KEYWORD=VALUE KEYWORD=VALUE ...]]
[-states ELECTRONIC_STATE [ELECTRONIC_STATE ...]] [-excited STATE]
[-cs_charge CHARGE] [-bonds] [-allow_hx USE_HX_BONDS]
[-include_smarts SMARTS [SMARTS ...]]
[-exclude_smarts SMARTS [SMARTS ...]] [-ligands] [-vertical]
[-use_formal_q] [-TPP THREADS] [-use_zip_data PATH]
[-restart_proj PROJECT_NAME] [-restart_disp INCORPORATION]
[-restart_viewname VIEWNAME] [-restart_host HOSTNAME:PROCESSORS]
[-restart_jobname JOBNAME] [-HOST <hostname>]
[reactant_file] [output_file]
Runs bond and ligand dissociation calculations with Jaguar. Reaction
structures are produced that contain the reactant and product molecules and a
bond dissociation energy property. Individual reactant and product fragment
structures are also produced. Reactions can be produced starting with the
reactant in the ground state, lowest triplet state, or as a radical cation or
anion. Duplicate structures are tracked so that only the minimum number of
Jaguar jobs are run. Copyright Schrodinger, LLC. All rights reserved.
positional arguments:
reactant_file The file with the reactant structure(s) (default:
None)
output_file The file that will contain all dissociation reaction
structures and energies (default: None)
options:
-h, -help Show this help message and exit.
-keywords KEYWORD=VALUE KEYWORD=VALUE [KEYWORD=VALUE KEYWORD=VALUE ...], -k KEYWORD=VALUE KEYWORD=VALUE [KEYWORD=VALUE KEYWORD=VALUE ...]
Jaguar keywords to include in calculations. Can be
given multiple keywords, ex. -k dftname=b3lyp
basis=midix... If this is the last flag before the
input/output file names, use -- to terminate the list
of keywords. (default: ['dftname=B3LYP',
'basis=LACV3P**', 'igeopt=1', 'iaccg=3', 'maxit=100',
'nofail=1', 'isymm=0', 'nops_opt_switch=10'])
-states ELECTRONIC_STATE [ELECTRONIC_STATE ...], -s ELECTRONIC_STATE [ELECTRONIC_STATE ...]
The electronic state of the reactant. "s0" is closed
shell ground state, "t1" is lowest triplet state,
"anion" is the 1-electron reduction form of the ground
state, "cation" is the 1-electron oxidation form of
the ground state, "excited" is an excited state, and
"s1" is the same as "-states excited -excited S1".
States with a charge and or an unpaired electron will
result in two output reactions for each fragmentation,
one where product A carries the charge/electron and
one where product B carries the charge/electron. If
this is the last flag before the input/output file
names, use "--" to terminate the list of states. This
flag interacts with "-cs_charge" to determine the
overall charge and multiplicity of the initial state.
For instance, "-states anion" and "-cs_charge 1" will
result in a neutral starting state with 1 unpaired
electron. Combinations that result in a charge of
+/-2, such as "-states anion" and "-cs_charge -1", are
not allowed. (default: ['s0'])
-excited STATE Indicate the state to be computed with -states
excited. Should be either Sx or Tx, where S or T
indicates singlet or triplet, and x indicates which
state of that spin. For instance, S1 to indicate the
first singlet excited state or T3 to indicate the 3rd
triplet state. (default: S1)
-cs_charge CHARGE The charge of the closed-shell molecule. Combinations
of -states and -cs_charge that result inan overall
charge of +/-2 are not allowed. See -states for more
information. (default: 0)
-bonds, -b Dissociate all single non-ring bonds. See also
-allow_hx_bonds (default: False)
-allow_hx USE_HX_BONDS
Include H-X bonds in bonds that should be dissociated.
Options are "no", "yes" or "only". "no" indicates that
H-X bonds should not be included (default). "yes"
indicates that H-X bonds should be included. "only"
indicates that ONLY H-X bonds should be included -
i.e. all reactions will be hydrogen abstractions.
(default: no)
-include_smarts SMARTS [SMARTS ...], -i SMARTS [SMARTS ...]
Only bonds to atoms that match the given SMARTS
patterns will be considered for dissociation. Multiple
SMARTS patterns may be given separated by spaces. If
this is the last argument before the input files,
terminate the list of patterns with a "--". (default:
None)
-exclude_smarts SMARTS [SMARTS ...], -e SMARTS [SMARTS ...]
Atoms that match the given SMARTS patterns will not be
be considered for dissociation. Multiple SMARTS
patterns may be given separated by spaces. If this is
the last argument before the input files, terminate
the list of patterns with a "--". (default: None)
-ligands, -l Dissociate transition metal ligands (default: False)
-vertical Compute vertical bond dissociation energies by
optimizing the reactant but freezing the products at
the reactant geometry. (default: False)
-use_formal_q Determine product charges based on the formal charges
of the atoms in the fragment. Formal charges must be
set on the atoms in the input structure and must equal
-cs_charge. (default: False)
-TPP THREADS Number of threads per MPI processor to use for each
Jaguar job. (default: 1)
Restart options:
-use_zip_data PATH Extract the archive before running. Any completed
files in the archive will be used instead of
submitting new jobs. (default: None)
-restart_proj PROJECT_NAME
Project name the restart job is associated with.
(default: None)
-restart_disp INCORPORATION
Incorporation state for the restart job. Should be one
of: append, ignore. (default: None)
-restart_viewname VIEWNAME
Viewname for the panel submitting the restart job.
Leave blank if running from the command line.
(default: None)
-restart_host HOSTNAME:PROCESSORS
Host for restart in the form of "hostname:cpus".
(default: None)
-restart_jobname JOBNAME
Jobname for restart. (default: None)
Job Control Options:
-HOST <hostname> Run job remotely on the indicated host entry.
(default: localhost)