Full keyword list

Below are tables with explanations for all WEASEL keywords. These tables are categorized according to the functions of the keywords. You can jump to the different categories using the list below:

Options

Keyword

Description
-h, --help
show this help message and exit
-v, -version, --version

show program's version number and exit
-settingsfile F
Use project settings. Give filename with absolute
path.
-postprocess
Do only post-processing, i.e. do not run the actual
jobs. Output files should be present.
-restart RESTART
Restart a previously partially finished job. The
entire job folder should still be available. Job is
restarted where incomplete output files are present.
-overwrite
Overwrite existing files and folders with the same
basename.
-no-overwrite
Do not overwrite any files and folders with the same
basename. If a mainjob folder with the same basename
exists and new one with an additional index number
will be created (e.g. '<basename>_1').

Structures

Primary chemical structure(s) used for calculations. filename Structure file with a single or multiple structures: Allowed formats : xyz, mol2, pdb, sdf, mae, smi and inchi

Keyword

Description
-smiles SMILES [SMILES ...]

Provide input structure(s) as list of SMILES strings.
Multiple SMILES strings should be separated by spaces.
-inchi INCHI [INCHI ...]

Provide input structure(s) as list of InChI strings.
Multiple InChIs strings should be separated by spaces.
-atom ATOM [ATOM ...]

Pass a single atom as input. Multiple atoms can be
separated by spaces. The charge and multiplicity can
be set via '-c' and '-m', respectively. All atoms will
receive the same charge and multiplicity!

Workflows

Standard workflows. (Custom workflow directory can be set via environment variable WEASEL_WORKFLOW_DIR)

Keyword

Description
-workflow W, -W W
Available workflows are: AIQU-ConfSearch, AIQU-
ConfSearch-Extended, AIQU-ConfSearch-Extended-v2,
AIQU-ConfSearch-v2, AIQU-NMS, AIQU-NMS-Extended, AIQU-
SP-ExcitedState, AIQU-SP-Solvent, CCS, CCS-Deprot-
Ensemble, CCS-Prot-Ensemble, ChemSearch-Deprot,
ChemSearch-HAT, ChemSearch-IonBinding, ChemSearch-
Prot, ChemSearch-Prot-Docker, ChemSearch-Tautomer,
ConfSearch, ConfSearch-ActiveSite, ConfSearch-TS,
Docking-Water, ExcitedState-Analysis, ExcitedState-
Opt, HostGuestLED, InteractionEnergy,
NormalModeSampling, OptimalBinding, React,
React_water, Reactivity, Reactivity-Explore, Spectrum-
IR, Spectrum-IR-Ensemble, Spectrum-NMR, Spectrum-NMR-
Ensemble, Spectrum-Raman, Spectrum-Raman-Ensemble,
Spectrum-UVVisCD, Spectrum-UVVisCD-Ensemble
-workflow-file WORKFLOW_FILE

path to custom workflow file.

System Settings

Keyword

Description
-keeptopo
Keep the topology (i.e. atom connectivity and bond
orders) of the input structure(s) if available.
-no-keeptopo
Discard any topology info (i.e. atom connectivity and
bond orders) given in the input structures.
-mirror
Mirror all conformer structures that do not have a
chiral center.
-no-mirror
Don't mirror all conformer structures that do not have
a chiral center.
-c C, -charge C
System charge C
-enforcefilecharge
Total charged defined in structure file, SMILES or
InChI is used, instead of the one defined via
'-c/-charge' or in the settings/workflow file.
-no-enforcefilecharge

Ignore Total charged defined in structure file, SMILES
or InChI is used. (This switch is only relevant if
enforcing of file charges is turned on by default in
the settings/workflow file!
-m M, -mult M
System multiplicity M
-temp T
Temperature T in Kelvin
-pressure P
Pressure P in atm

Basic Workflow Options

Keyword

Description
-opt-sp
Optimization and SP energy calculation
-sponly
Only do SP calculation, no optimization
-optts-activeatoms A [A ...]

Active atoms of transition state, i.e. atoms that are
involved in reaction.
-optts-activeatoms-template A [A ...]

Active atoms of transition state of template Hessian
(specified via -optts-inputhessian), i.e. atoms that
are involved in reaction.
-preopt
Switch on preoptimization
-no-preopt
Switch off preoptimization
-opt
Switch on optimization
-no-opt
Switch off optimization and preoptimization
-correctimagmodes
Rerun optimization in case (unwanted) imaginary modes
are found with the frequency analysis.
-no-correctimagmodes
Do not rerun optimization in case (unwanted) imaginary
modes are found with the frequency analysis.
-opt-convergence {Sloppy,Loose,Normal,Tight,VeryTight}

Convergence level used for optimization. Allowed
options are: Sloppy, Loose, Normal, Tight, VeryTight
-opt-calcinitialhess
Calculate an initial exact Hessian before
optimizations
-opt-retry
Try to convergence a non-converged optimization by
running a few extra cycles.
-opt-no-retry
Do not try to convergence a non-converged optimization
by any means.
-spdft
Do a final DFT single point calculation
-no-spdft
Switch off DFT single point calculation
-spdft-grad
Compute gradient in DFT single point calculation
-no-spdft-grad
Switch off gradient calculation in DFT single point
calculation
-optts
do TS optimization
-optts-inputhessian INPUTHESSIAN

Input hessian of (previously optimized) TS structure.
Needs to be an ORCA Hessian file.
-spwf
Switch on Post-HF single point calculation
-no-spwf
Switch off Post-HF single point calculation
-scants
Do relaxed surface scan and subsequent TS optimization
-freq
Compute vibrational frequencies at the end of a (TS)
optimization
-no-freq
Do not compute vibrational frequencies, e.g. at the
end of a (TS) optimization
-irc
Compute intrinsic reaction coordinate
-no-irc
Do not compute intrinsic reaction coordinate, e.g. at
the end of a TS optimization
-sn SN
Rotational symmetry number. Overwriting the
automatically detected rotational symmetry number.
-reactivity-en
Compute electro- and nucleophilicity
-uhf
Force unrestricted calculation
-no-d3
Switch off D3
-fukui
Compute Fukui function on DFT SP level.

Methods

Keyword

Description
-preopt-method M
Method used for preoptimization. Allowed options M
are: XTB, XTB1, XTB-FF, HF-3c, PBEh-3c, B97-3c,
r2SCAN-3c, AM1, PM3, MNDO
-preopt-keeptopology
The connectivity of the input structure cannot change
during preoptimization.
-no-preopt-keeptopology

The connectivity of the input structure can change
during preoptimization.
-opt-method M
Method used for optimization. Allowed options M are:
BP86, TPSS, PBE, B97M-D3BJ, B3LYP, B3LYP/G, BHANDHLYP,
PW6B95, PBE0, wB97X, wB97X-V, wB97M-V, CAM-B3LYP,
B2PLYP, DLPNO-B2PLYP, B2GP-PLYP, DLPNO-B2GP-PLYP, DSD-
PBEP86, DLPNO-DSD-PBEP86, DSD-PBEP86/2013, DLPNO-DSD-
PBEP86/2013, R2SCAN, M062X, MP2, DLPNO-MP2, SCS-MP2,
RIJDX-MP2, RIJDX-DLPNO-MP2, RIJDX-SCS-MP2, RIJK-MP2,
RIJK-DLPNO-MP2, RIJK-SCS-MP2, XTB, XTB1, XTB-FF,
HF-3c, PBEh-3c, B97-3c, r2SCAN-3c, AM1, PM3, MNDO
-spdft-method M
Method used for DFT single point calculation. Allowed
options M are: BP86, TPSS, PBE, B97M-D3BJ, B3LYP,
B3LYP/G, BHANDHLYP, PW6B95, PBE0, wB97X, wB97X-V,
wB97M-V, CAM-B3LYP, B2PLYP, DLPNO-B2PLYP, B2GP-PLYP,
DLPNO-B2GP-PLYP, DSD-PBEP86, DLPNO-DSD-PBEP86, DSD-
PBEP86/2013, DLPNO-DSD-PBEP86/2013, R2SCAN, M062X,
HF-3c, PBEh-3c, B97-3c, r2SCAN-3c, AM1, PM3, MNDO
-spwf-method M
Method used for Post-HF single point calculation.
Allowed options M are: HF, MP2, SCS-MP2, CCSD,
CCSD(T), DLPNO-MP2, DLPNO-CCSD, BP-DLPNO-CCSD, DLPNO-
CCSD(T), BP-DLPNO-CCSD(T), RIJDX-HF, RIJDX-MP2, RIJDX-
SCS-MP2, RIJDX-DLPNO-MP2, RIJDX-DLPNO-CCSD(T), RIJK-
HF, RIJK-MP2, RIJK-SCS-MP2, RIJK-DLPNO-MP2, RIJK-
DLPNO-CCSD(T), CCSD_T, DLPNO-CCSD_T, BP-DLPNO-CCSD_T,
RIJDX-DLPNO-CCSD_T, RIJK-DLPNO-CCSD_T
-spwf-pno P PNO
Settings for Post-HF single point calculation.
Allowed options P are: Loose, Normal, Tight,
Normal_TightPairs,
LooseIntra_NormalTightPairsForInteraction,
LooseIntra_TightForInteraction,
NormalIntra_NormalTightPairsForInteraction,
NormalIntra_TightForInteraction
-spdft-pno P PNO
Settings for DLPNO-DHDFT single point calculation.
Allowed options P are: Loose, Normal, Tight
-opt-pno P PNO
Settings for DLPNO-DHDFT optimizations. Allowed
options P are: Loose, Normal, Tight
-no-cosx
Do not use COSX approximation
-rijk
Use RIJK approximation
-conf-no-keeptstopo
The connectivity of the TS active atoms can change
during optimization.
-conf-preopt-method M

Method used for preoptimization in conformational
search. Allowed options see: see: -preopt-method
-conf-looseopt-method M

Method used for loose optimization in conformational
search. Allowed options see: -opt-method
-conf-opt-method M
Method used for optimization in conformational search.
Allowed options see: -opt-method
-conf-spdft-method M
Method used for DFT single point calculation in
conformational search. Allowed options see: -spdft-
method
-conf-spwf-method M
Method used for Post-HF single point calculation in
conformational search. Allowed options see: -spwf-
method
-nmr-coupling-method M

Method used for NMR J-coupling calculation. Allowed
options see: -spdft-method

Basis Sets

Keyword

Description
-opt-basis BAS
Basis used for optimization. Allowed options BAS are:
MiniX, SV, SV(P), SVP, TZVP, TZVPP, old-SV, old-SV(P),
old-SVP, old-TZVP, old-TZVPP, def2-SV(P), def2-SVP,
def2-TZVP, def2-TZVP(-F), def2-TZVPP, def2-QZVP,
def2-QZVPP, ma-def2-SV(P), ma-def2-SVP, ma-def2-TZVP,
ma-def2-TZVP(-F), ma-def2-TZVPP, ma-def2-QZVP, ma-
def2-QZVPP, def2-SVPD, def2-TZVPD, def2-TZVPPD,
def2-QZVPD, def2-QZVPPD, ZORA-SV(P), ZORA-SVP, ZORA-
TZV(P), ZORA-TZVP, ZORA-TZVPP, ZORA-def2-SV(P), ZORA-
def2-SVP, ZORA-def2-TZVP, ZORA-def2-TZVP(-F), ZORA-
def2-TZVPP, ZORA-def2-QZVPP, old-ZORA-SV(P), old-ZORA-
SVP, old-ZORA-TZV(P), old-ZORA-TZVP, old-ZORA-TZVPP,
ZORA-ma-def2-SV(P), ZORA-ma-def2-SVP, ZORA-ma-
def2-TZVP, ZORA-ma-def2-TZVP(-F), ZORA-ma-def2-TZVPP,
ZORA-ma-def2-QZVPP, DKH-SV(P), DKH-SVP, DKH-TZV(P),
DKH-TZVP, DKH-TZVPP, DKH-def2-SV(P), DKH-def2-SVP,
DKH-def2-TZVP, DKH-def2-TZVP(-F), DKH-def2-TZVPP, DKH-
def2-QZVPP, old-DKH-SV(P), old-DKH-SVP, old-DKH-
TZV(P), old-DKH-TZVP, old-DKH-TZVPP, DKH-ma-
def2-SV(P), DKH-ma-def2-SVP, DKH-ma-def2-TZVP, DKH-ma-
def2-TZVP(-F), DKH-ma-def2-TZVPP, DKH-ma-def2-QZVPP,
SARC-DKH-TZVP, SARC-DKH-TZVPP, SARC-ZORA-TZVP, SARC-
ZORA-TZVPP, cc-pVDZ, cc-pVTZ, cc-pVQZ, cc-pV5Z, cc-
pV6Z, aug-cc-pVDZ, aug-cc-pVTZ, aug-cc-pVQZ, aug-cc-
pV5Z, aug-cc-pV6Z, pcSseg-0, pcSseg-1, pcSseg-2,
pcSseg-3, pcSseg-4, pcJ-0, pcJ-1, pcJ-2, pcJ-3, pcJ-4,
6-31+G*, 6-31+G**, 6-31G*, 6-31G**, 6-311+G**
-spdft-basis BAS
Basis used for DFT single point calculation. Allowed
options see: -opt-basis
-spwf-basis BAS
Basis used for Post-HF single point calculation.
Allowed options see: -opt-basis
-opt-basis2 BAS
Extra basis used for optimization. Allowed options
see: -opt-basis
-spdft-basis2 BAS
Extra basis used for DFT single point calculation.
Allowed options see: -opt-basis
-spwf-basis2 BAS
Extra basis used for Post-HF single point calculation.
Allowed options see: -opt-basis
-basis2-atoms A [A ...]

Atoms that are described by the extra basis. Atom
index ranges can be defined via A-B or A- (up to end
of system).
-conf-looseopt-basis BAS

Basis used for loose optimization in conformational
search. Allowed options see: -opt-basis
-conf-opt-basis BAS
Basis used for optimization in conformational search.
Allowed options see: -opt-basis
-conf-spdft-basis BAS

Basis used for DFT single point calculation in
conformational search. Allowed options see: -opt-basis
-conf-spwf-basis BAS
Basis used for Post-HF single point calculation in
conformational search. Allowed options see: -opt-basis
-nmr-coupling-basis BAS

Basis used for NMR J-coupling calculation. Allowed
options see: -spdft-basis

Implicit Solvation

Keyword

Description
-solvent SOL
Define solvent to be used with implicit solvation
model. If explicit solvation is turned on, it will use
the same solvent as defined through the explict
solvation, as long as no custom explicit solvent is
specified. Allowed options SOL are: Acetone,
Acetonitrile, Ammonia, Benzene, CCl4, CH2Cl2, CHCl3,
Chloroform, Cyclohexane, DMF, DMSO, Ethanol, H2O,
Hexane, Infinity, Methanol, NH3, Octanol, Protein,
Pyridine, THF, Tetrahydrofuran, Toluene, Water
-solvent-spwf-method TYPE

define method to be used with implicit solvation model
+ coupled cluster. Allowed options are: None, PTE,
PTE(S), PTES
-gas
Switch off solvent
-smd
Use implicit solvent SMD
-cpcm
Use implicit solvent CPCM (using COSMO epsilon
function).

Explicit Solvation

Keyword

Description
-solvent-expl [XYZFILE]

Perform explicit solvation. The default solvent is the
same one used for implicit solvation. If implicit
solvation is turned off, water will be used as
solvent.Optionally a different explicit solvent can be
read from XYZFILE.
-solvent-no-explicit
Turn off explicit solvation.
-solvent-expl-only [XYZFILE]

Only perform explicit solvation of solute and exit.
The default solvent is the same one used for implicit
solvation. If implicit solvation is turned off, water
will be used as solvent. Optionally a different
explicit solvent can be read from XYZFILE.
-solvent-expl-method {docking,stochastic}

Method used for explicit solvation.
-solvent-expl-nsolv N

Number of solvent molecules to be added.
-solvent-expl-fixsolute

Keep the geometry of the solute fixed during explicit
solvation.
-solvent-expl-no-fixsolute

Do not keep the geometry of the solute fixed during
explicit solvation.
-solvent-expl-charge N

Total charge of solvent molecule.
-solvent-expl-mult N
Multiplicity of solvent molecule.
-solvent-expl-maxrad N

Fixed maximum radius for the explicit solvent [Ang].
-solvent-expl-droplet

Enforce a spherical arrangement of solvent molecules
around the solute.
-solvent-expl-no-droplet

Do not enforce a spherical arrangement of solvent
molecules around the solute.
-solvent-expl-auto-sp-method M

Method M used for DFT single point calculations used
to evaluate which solvent molecules are strongly
bound. Allowed options see: -spdft-method
-solvent-expl-auto-sp-basis BAS

Basis set BAS used for DFT single point calculations
used to evaluate which solvent molecules are strongly
bound. Allowed options see: -opt-basis
--solvent-expl-auto-sp-final-method M

Method M used for DFT single point calculations used
to evaluate the final binding energy solute and
solvents. Allowed options see: -spdft-method
-solvent-expl-auto-sp-final-basis BAS

Basis set BAS used for DFT single point calculations
used to evaluate the final binding energy solute and
solvents. Allowed options see: -opt-basis
-solvent-expl-auto-maxmol N

Maximum number of explicit solvent molecules to be
added. By default 150% of the number of atoms in the
solute molecule is the upper limit. But at least 10
molecules.
-solvent-expl-auto-batchsize N

Number of explicit solvent molecules added per
solvation cycle after the first cycle.
-solvent-expl-auto-inibatch N

Number of explicit solvent molecules added in the
first solvation cycle. By default this value is set to
the square root of the number of atoms in the solute
molecule is used. But a minimum of 5 solvent molecule
will be added in the first cycle.
-solvent-expl-auto-thresh N

Energy threshold (in kcal/mol) below which solvent
molecules are considered strongly bound.

Hardware

Keyword

Description
-cores N
Number of cores N for parallel run
-hostfile HOSTFILE
hostfile containing hostnames of reserved nodes (only
for calculations on computer cluster).
-mem
N[unit] Available memory per core. Allowed SI unit suffixes:
B, K, M, G, T [default: M]. Units are interpreted as
powers of 1000 (SI format).
-mem-total
N[unit] Available memory for all cores. Allowed SI unit
suffixes: B, K, M, G, T [default: M]. Units are
interpreted as powers of 1000 (SI format).

Output Options

Keyword

Description
-no-write-xyz
write a summary xyz file to the main job dir and for a
confsearch workflow intermediate ensembles to the
ConfSearch folder.
-write-mae, -write-maestro

write a summary maestro file to the main job dir and
for a confsearch workflow intermediate ensembles to
the ConfSearch folder.
-write-sdf
write a summary sdf file to the main job dir and for a
confsearch workflow intermediate ensembles to the
ConfSearch folder.
-verbosesummary
write a verbose version of the summary file.
-label L
Directory label for where calculation output is
stored. Label is added to basename.
-outputmolversion {V2000,V3000}

Define mol version used for output of sdf files.
[Default: if the structure file is a sdf file, then
the same version like in the file is used, otherwise
V3000.]
-reportdir REPORT_DIR

Write a copy of the report files to REPORT_DIR. Can
also be set via $WEASEL_REPORT_DIR.
-basename BASENAME
Set a basename for the current job. Normally Weasel
determines the basename automatically from the input
parameters.
-energyunit
eU Unit for energy in reporting. Allowed options eU are:
Eh, J, J/mol, au, cal, cal/mol, eV, kJ, kJ/mol, kcal,
kcal/mol, keV
-chargetype cT [cT ...]

Population scheme that is used for charge printing in
mol2 file. Not used for SP_WF calculations. Allowed
options cT are: CHELPG, Hirshfeld, Loewdin, Mulliken,
all
-storecharges
Store charges specified via -chargetype in charges.txt
file.
-storewfx
Store wfx and wfx file for SPDFT calculations.
-compress {files,folders}

Choose a compression mode. Modes: 'files'=Only
compress large files; 'folders'=Tar and compress all
calculation dirs.
-no-compress
Disable compression.

Relaxed Surface Scan Options

Keyword

Description
-scan-bond A A
Bond definition for relaxed surface scan. A1 A2.
-scan-angle A A A
Angle definition for relaxed surface scan. A1 A2 A3.
-scan-dihedral A A A A

Dihedral definition for relaxed surface scan. A1 A2 A3
A4.
-scan-start V
Start value V for scan
-scan-stop V
End value V for scan
-scan-nsteps N
Number of steps N for scan

Constraints Options

Keyword

Description
-constrain-cartesians A [A ...]

Constrain the current Cartesian coordinates of
selected atoms. Atoms can either specified by their
atom type (element), by their atom id or by a ranges
of atom ids: "-constrain-cartesians C H 1 2 5-8" would
constrain all carbon and hydrogen atoms, as well as
the atoms 1, 2, 5, 6, 7 and 8. Counting of atoms
usually starts from 1.
-constrain-bonds A1[:A2[:Value]] [A1[:A2[:Value]] ...]

Constrain selected bonds. If only the first atom A1 is
specified all bonds to that atom are constrained. The
single atom can either by specified by its id
(counting usually starts from 1) or by its atom type
(element). If the latter syntax is used all atoms of
that type are considered. If A1 and A2 are specified
the bond between these two atoms is constrained to the
current value. Alternatively the bond length in
Angstrom can be given as third argument Value.
Multiple constraints can be specified as list: e.g.
"-constraint-bond C 1:2 3:4:2.0" would constraint all
bonds to atoms of type C, the bond between atom 1 and
2 and constrain the bond between atom 3 and 4 to 3.0
Angstrom. If multiple constraints are defined that
overlap, then only the last one is considered!
-constrain-angles A1:[Value]|A1:A2:A3:[Value] [A1:[Value]|A1:A2:A3:[Value] ...]

Constrain selected angles. If only a single atom A1 is
specified all angles where A1 is the central atoms are
constrained. Alternatively a specific angle can be
specified by providing all three atoms A1, A2 and A3.
Atoms are specified by their atomic id. Counting
usually starts from 1. Angles are expected to be given
in degrees. The items within a single constraint
statement have to be separated by ":". The Value is
optional. If Value is not specified the current
value(s) of the angle(s) are used. Multiple constraint
can be specified at once, by separating the statements
by spaces: E.g. "-constrain-angles 1:2:3 5:6:7:120 8
9:50 " would constrain the angle between atoms 1, 2
and 3 to its current value, the angle formed by 5, 6
and 7 to 120°, all angles that have atom 8 as central
atom to their current value and all angles that have
atom 5 as central atom to 50°. If multiple constraints
are defined that overlap, then only the last one is
considered!
-constrain-dihedrals A1:A2:[Value]|A1:A2:A3:A4:[Value] [A1:A2:[Value]|A1:A2:A3:A4:[Value] ...]

Constrain selected dihedrals. If only two atoms A1 and
A2 are specified all dihedrals where A1-A2 is the
central bond are constrained. Alternatively a specific
dihedral can be specified by providing all four atoms
A1, A2, A3 and A4. Atoms are specified by their atomic
id. Counting usually starts from 1. Dihedrals are
expected to be given in degrees. The items within a
single constraint statement have to be separated by
":". The Value is optional. If it is not specified the
current value(s) of the dihedrals(s) are used.
Multiple constraints can be specified at once, by
separating the statements by spaces: E.g. "-constrain-
dihedrals 1:2:3:4 5:6:7:8:109.4 9:10 11:12:123" would
constrain the dihedral formed by atoms 1, 2, 3 and 4
to its current value, the dihedral formed by 5, 6, 7
and 8 to 109.4°, all dihedrals that have the atoms 9
and 10 as central atoms to their current values and
all dihedrals that have the atoms 11 and 12 as central
atoms to 123.0°. If multiple constraints are defined
that overlap, then only the last one is considered!
-opth
optimize hydrogen positions only.
-constrain-xtbonly
Apply constraints only when using XTB level
optimization. Can be useful when XTB is too inaccurate
for specific bonds

Plot Options

Keyword

Description
-plot-mo N [N ...]
Plot Molecular Orbital Number N1 N2 for DFT SP
calculation.
-plot-ed
Plot Electron Density for DFT SP calculation.
-plot-sd
Plot Spin Density for DFT SP calculation.
-plot-lumo
Plot LUMO for DFT SP calculation.
-plot-homo
Plot HOMO for DFT SP calculation.
-plot-somo, -plot-somos

Plot SOMOs for DFT SP calculation.
-plot-fmos
Plot HOMO and LUMO for DFT SP calculation.
-plot-fmos-upto PLOTFMOSUPTO

Plot frontier orbitals for DFT SP calculation. Number
defines the HOMOs and LUMOs in both directions.
-grid-res N
Grid resolution, i.e. number of grid points per
Angstrom (x, y and z direction) for plots (MOs, ED,
SD).
-grid-x N
Number of grid points in x direction for plots (MO,
ED, SD).
-grid-y N
Number of grid points in y direction for plots (MO,
ED, SD).
-grid-z N
Number of grid points in z direction for plots (MO,
ED, SD).
-grid-xmin N
Minimum dimension on the x axis in Angstrom.
-grid-ymin N
Minimum dimension on the y axis in Angstrom.
-grid-zmin N
Minimum dimension on the z axis in Angstrom.
-grid-xmax N
Maximum dimension on the x axis in Angstrom.
-grid-ymax N
Maximum dimension on the y axis in Angstrom.
-grid-zmax N
Maximum dimension on the z axis in Angstrom.
-grid-xyzmin N
Minimum dimension on x, y and z axis in Angstrom.
-grid-xyzmax N
Maximum dimension on x, y and z axis in Angstrom.
-plot-format P
Output format for plots (MO, ED, SD). Allowed options
P are: cube, vis
-spectrum-npoints N
Number of data points for generating spectrum plots.
-spectrum-lineshape {GAUSSIAN,LORENTZIAN}

Lineshape function for spectrum peak broadening.
-spectrum-linewidth L

Linewidth for spectrum plots (in eV for UV/Vis/CD,
1/cm for IR/Raman, Hz for NMR).

BSSE Options

Keyword

Description
-bsse
Do BSSE calculation.
-bsse-gcp
Do a BSSE calculation using the DFT-D3-gCP scheme.
-bsse-bb
Do a BSSE calculation using the Boys-Bernardi scheme.
-no-bsse
Do not do a BSSE calculation (even if defined in
settings).
-bsse-c C1 C2 C1 C2
Only applicable if the docker is NOT used: Charges C1
and C2 for the two molecules of BSSE calculation. C1
is for the larger molecule (1), C2 for the smaller
molecule (2). If both molecules consist of the same
number of atoms, the molecule the first atom of the
system belongs to is molecule 1. Default is system
charge / 2.
-bsse-m M1 M2 M1 M2
Only applicable if the docker is NOT used:
Multiplicities M1 and M2 for the two molecules of BSSE
calculation. For ordering see bsseC. Default: Unpaired
electrons of system are divided equally onto both
molecules.
-bsse-dimercalcsonly
Do only the calculations for the dimer part, i.e. no
monomer calculations.
-bsse-freezemonomers BSSE
calculation: Do not separately optimize the
monomers, but instead use their geometries in the
complex.
-bsse-optimizemonomers

BSSE calculation: Do separately optimize the monomers.

Host-GuestAtom LED Options

Keyword

Description
-hg-led
Do host-guest LED calculation.
-no-hg-led
Do not do a host-guest LED calculation (even if
defined in settings).
-hg-led-dimercalcsonly

Do only the calculations for the dimer part, i.e. no
monomer calculations.
-hg-led-freezemonomers

Host-guest LED calculation: Do not separately optimize
the monomers, but instead use their geometries in the
complex.
-hg-led-optimizemonomers

Host-guest LED calculation: Do separately optimize the
monomers.
-hg-led-addguest AddGuest [AddGuest ...]

Add guest molecule to host: Need structure file.
Optional: 1) Charge of the guest: -C <charge> (default
0). 2) Multiplicity of the guest: -M <multiplicity>
(default 1).

Converger Options

Keyword

Description
-prescf
Converge the SCF with an approximate SCF before the
actual SP energy calculation
-no-prescf
Do not converge the SCF with an approximate SCF before
the actual SP energy calculation
-scf-retry
Try to recover non-convergence SCF calculation by
rerunning the SCF calculation with different SCF
acceleration strategies (see the '-badconvX' options
for more details).
-scf-no-retry
Do not try to recover a non-converged SCF calculation.
-no-badconv
Turn off any convergence accelerator ('-badconvX'
switches) and use ORCA's internal defaults.
-badconv1
Convergence accelerator when SCF convergence is very
slow with default settings. Invokes a smaller level
shift.
-badconv2
Convergence accelerator when SCF is fluctuating with
default settings. Increases damping, recomputes Fock
matrix after each iteration to reduce numerical noise.
-badconv3
Convergence accelerator when the SCF is unstable and
oscillating with default settings. Invokes a large
level shift.
-badconv4
Convergence accelerator for very tricky open-shell
systems. Performs first a small basis followed by the
final basis calculation.
-scf-trah-autotrah
Enable ORCA's AutoTRAH feature. AutoTRAH triggers TRAH
if a SCF is not converged after N cycles. N can be set
with '--scf-trah-autoiter'.
-scf-trah-no-autotrah

Disables ORCA's AutoTRAH.

Relativistics

Keyword

Description
-zora
Use ZORA for treatment of relativistic effects.
-dkh
Use DKH for treatment of relativistic effects.
-ecp
Use ECPs for treatment of relativistic effects.
-no-rel
Do not use scalar relativistics / ECPs.

Reactivity

Keyword

Description
-reactivity-nebts
Find TS with NEB-TS Feature
-product PRODUCT
File with product structure for finding TS.
-tsguess TSGUESS
File with TS guess structure for finding TS
(optional).
-neb-usemepguess
Use guess for minimum energy path in NEB calculation.
Guess provided in ORCA's allxyz file format as input
structure file.
-neb-fixends
Reactant and product structure should be kept as they
are.
-neb-sp-onlyts
If requested, compute SP and frequency only for TS
structure. (Not yet functional.)
-neb-sp-fullreaction
If requested, compute SP and frequency for reactant,
TS, and product.)
-neb-boost
Use Fast-NEB-TS to boost the convergence. Comes with
slightly lower robustness.
-neb-nimages NEB_NIMAGES

Use this number of images for the NEB calculation.
-irc-nsteps IRC_NSTEPS

Use this maximum number of steps for each direction of
the IRC calculation.
-irc-inputhessian IRC_INPUTHESSIAN

Input hessian of (previously optimized) TS structure
for IRC calculation. Needs to be an ORCA Hessian file.

Normal Mode Sampling

Keyword

Description
-nms
Do a Normal Mode Sampling (NMS)
-no-nms
Switch off Normal Mode Sampling (NMS)
-nms-nstruc NMSNSTRUC

Number of structures to generate with NMS
-nms-nmodes NMSNMODES

Number of normal modes to use for the displacement
-nms-temp NMSTEMP
Temperature used in normal mode sampling
-nms-unit {regular,unitless}

Units of the normal modes used
-nms-usegaussianw
Use Gaussian weights on top of the regular Ri
-nms-sigma NMSSIGMA
Sigma value for the Gaussian weight (in cm-1)
-nms-minfreq NMSMINFREQ

Minimum frequency of mode to include (in cm-1)

UV/Vis and CD calculation

Keyword

Description
-uvvis
Start TDDFT calculation for UV/Vis spectrum
prediction.
-es-states TDDFT_NROOTS

Number of excited states considered for UV/Vis / CD
spectrum prediction.
-es-soc
Compute Spin-Orbit-Coupling between the states.
-es-analyzestates TDDFT_ANALYZE_ROOTS [TDDFT_ANALYZE_ROOTS ...]

Which excited states should be analyzed? Options: All,
or provide a list of integers.
-es-densityanalysis {None,Unrelaxed,Relaxed,Both}

Which density should be used for excited state
population analysis (atomic charges, bond orders)?
Options:None, Unrelaxed, Relaxed, Both
-es-opt
Optimize to excited state.
-es-opt-state TDDFT_OPT_STATE

Optimize to excited state.
-es-opt-triplet
Optimize to triplet state in excited state
optimization (for singlet ground states).
-tddft-tda
Use TDA approximation for TDDFT.
-tddft-no-tda
Do not use TDA approximation for TDDFT.

IR calculation

Keyword

Description
-ir
Compute IR spectrum
-raman
Compute Raman spectrum (also implies IR)
-ir-scalefreq F
Scale the harmonic frequencies by F before generating
IR/Raman spectra

NMR Properties

Keyword

Description
-nmr [{element,all} ...]

Compute NMR chemical shifts for a list of elements or
"all". If no element is defined, default is H and C.
-nmr-ref-h NMR_REF_H NMR
reference for H: value in ppm or structure file.
-nmr-ref-c NMR_REF_C NMR
reference for C: value in ppm or structure file.
-nmr-ref-n NMR_REF_N NMR
reference for N: value in ppm or structure file.
-nmr-ref-si NMR_REF_SI

NMR reference for Si: value in ppm or structure file.
-nmr-ref-p NMR_REF_P NMR
reference for P: value in ppm or structure file.
-nmr-ref-{x} NMR_REF_X

NMR reference (value in ppm or structure file) for
another element. Replace {x} with an element symbol in
lowercase.
-nmr-coupling [{element,all} ...]

Compute NMR indirect spin-spin couplings for a list of
elements or "all". If no element is defined, default
is H.

Collision Cross Section

Keyword

Description
-ccs
Do a Collision Cross Section Calculation (CCS).
-no-ccs
Switch off Collision Cross Section Calculation (CCS)
-ccs-cluster
Do a geometrical clustering before CCS calculations
-ccs-no-cluster
Switch off geometrical clustering before CCS
calculations
-ccs-maxcycles CCSMAXCYCLES

Maximum number of cycles to run with CCS
-ccs-mincycles CCSMINCYCLES

Minimum number of cycles to run with CCS
-ccs-velocity CCSVELOCITY

Number of velocities to run with CCS
-ccs-impact CCSIMPACT

Number of impact integration points to run with CCS
-ccs-gas {He,N2}
Type of collision gas to run with CCS. Allowed options
are: He, N2
-ccs-sem CCSSEM
Relative deviation of the standard error of the mean.
-ccs-slope CCS_SLOPE
Slope value for linear calibration of CCS values.
-ccs-offset CCS_OFFSET

Offset value for calibration of CCS values.

GOAT - used in ConfSearch only

Keyword

Description
-goat-explore
Set GOAT-EXPLORE option for a complete search with
free topology.
-goat-entropy
Set GOAT-ENTROPY option to enforce convergence of
conformational entropy.
-goat-diversity
Set GOAT-DIVERSITY option to focus on geometrical
diversity.
-goat-react
Set GOAT-REACT option to allow for full PES search
(still experimental!).
-goat-react-maxtopodiff CONF_GOAT_MAXTOPODIFF

Define the maximum topological difference for a GOAT-
REACT run (default 8 - still experimental!).
-goat-nworkers CONF_GOAT_NWORKERS

Define the number of workers used in the GOAT. Default
is AUTO.
-goat-freefragments
Free topology between different fragments
-goat-freezeamides
Freeze cis/trans amide chirality change when using
GOAT.
-goat-freezecistrans
Freeze cis/trans double bond chirality change when
using GOAT.
-goat-maxcn ID/ELEMENT:CN [ID/ELEMENT:CN ...]

For conformer searcher with GOAT, constrain maximum
coordination number (CN) for individual atoms. Two
syntaxes are allowed to specify the max CN: 1) ID:CN,
e.g. 3:4, where ID is the position of the atom in the
input file (counting starts from 1) and CN is the
coordination number; 2) ELEMENT:CN, e.g. Mn:5, where
all atoms of type ELEMENT will have a maximum CN of 5.
To specify multiple entries, separate them by spaces:
e.g. 5:3 C:4 ...
-goat-scaleiter GOAT_SCALEITER

Define the scaling factor for the number of GOAT
optimizations.

Ensemble Workflow

Keyword

Description
-boltzmannaverage
Calculate Boltzmann-weighted average properties or
spectra using multiple structures from input or
conformer search (with CONF_NFinal > 1).

Software Settings

Keyword

Description
-scratchdir DIR
set a scratch directory for your WEASEL job.

Multiscale Simulations

Keyword

Description
-ms-setup
Set up multiscale system, without running actual
calculations.
-ms-qmmm
Run QMMM calculation, including on-the-fly setup.
-ms-setup-interactive

Set up multiscale system interactively.
-ms-enforce-input-charge

After multiscale setup do not update QM region charge,
but use user input charge
-ms-orcafffile ORCAFF

ORCA forcefield file, accompanying structure file.
-ms-qc-add-res R [R ...]

Residues defining core region of QM region. Can be
residue name or residue ID. If the residue name occurs
more than once in the pdb file, only the residue ID is
accepted - but this can be given for multiple
residues. If the residue ID occurs more than once, the
corresponding segment (SEG) needs to be defined as
well via SEG-ID.
-ms-qc-add-atom A [A ...]

Atoms defining core region of QM region. Can be atom
name or atom ID. If the atom name occurs more than
once in the pdb file, only the atom ID is accepted -
but this can be given for multiple atoms.
-ms-qc-ext-by X
QM region is constructed by extending QM core region
by X Angstrom.
-ms-qc-ext-by-full-res

Extend QM core region by full residues.
-ms-qc-ext-by-sc
Extend QM core region by side chains only.
-ms-qc-ext-by-polar-groups

Extend QM core region by polar groups only, ignoring
nonpolar side chains.
-ms-qc-ext-by-polar-interactions

Extend QM core region by polar interactions only, e.g.
hydrogen bonds and salt bridges.
-ms-qc-ext-no-autocorrect

Switch off automatic check for MM backbone gaps
between neighboring QM sidechains or QM backbones.
Checks whether less than three bonds separate two
QM/MM boundaries.
-ms-qr-add-atom A [A ...]

Add atom to automatically generated QM region. Can be
atom name or atom ID.
-ms-qr-add-res R [R ...]

Add residues to automatically generated QM region. Can
be residue name or residue ID.
-ms-qr-add-sc R [R ...]

Add side chains to automatically generated QM region.
Can be residue name or residue ID.
-ms-qr-add-bb R [R ...]

Add backbone to automatically generated QM region. Can
be residue name or residue ID.
-ms-qr-rm-atom A [A ...]

Add atom to automatically generated QM region. Can be
atom name or atom ID.
-ms-qr-rm-res R [R ...]

Remove residues from automatically generated QM
region. Can be residue name or residue ID.
-ms-qr-rm-sc R [R ...]

Remove side chains from automatically generated QM
region. Can be residue name or residue ID.
-ms-qr-rm-bb R [R ...]

Remove backbone from automatically generated QM
region. Can be residue name or residue ID.
-ms-qr-file F
Atoms for QM region are provided via a file.
-ms-ac-add-res R [R ...]

Residues defining core region of active region. Can be
residue name or residue ID. If the residue name occurs
more than once in the pdb file, only the residue ID is
accepted - but this can be given for multiple
residues. If the residue ID occurs more than once, the
corresponding segment (SEG) needs to be defined as
well via SEG-ID.
-ms-ac-add-atom A [A ...]

Atoms defining core region of active region. Can be
atom name or atom ID. If the atom name occurs more
than once in the pdb file, only the atom ID is
accepted - but this can be given for multiple atoms.
-ms-ac-ext-by X
Active region is constructed by extending active core
region by X Angstrom.
-ms-ac-ext-by-wat-and-h

Extend active core region by water residues and
hydrogens only.
-ms-ac-ext-by-h
Extend active core region by hydrogens only.
-ms-ac-ext-by-sc-and-bb-sep

Extend active core region by side chain and backbone
groups separately.
-ms-ac-ext-by-full-res

Extend active core region by full residues.
-ms-ar-fixbb
Extend active core region by side chains only.
-ms-ar-add-atom A [A ...]

Add atom to automatically generated active region. Can
be atom name or atom ID.
-ms-ar-add-res R [R ...]

Add residues to automatically generated active region.
Can be residue name or residue ID.
-ms-ar-add-sc R [R ...]

Add side chains to automatically generated active
region. Can be residue name or residue ID.
-ms-ar-add-bb R [R ...]

Add backbone to automatically generated active region.
Can be residue name or residue ID.
-ms-ar-rm-atom A [A ...]

Remove atom from automatically generated active
region. Can be atom name or atom ID.
-ms-ar-rm-res R [R ...]

Remove residues from automatically generated active
region. Can be residue name or residue ID.
-ms-ar-rm-sc R [R ...]

Remove side chains from automatically generated active
region. Can be residue name or residue ID.
-ms-ar-rm-bb R [R ...]

Remove backbone from automatically generated active
region. Can be residue name or residue ID.
-ms-ar-cut-bb-option T

Scheme for cutting backbone in active core and region.
Allowed options are: chemical, residueDefinition
-ms-ac-eq-to-qc
For active core region use the same atoms/residues as
for the QM core region.
-ms-ar-eq-to-qr
For active region use the same atoms/residues as for
the QM region.
-ms-ar-file F
Atoms for active region are provided via a file.

Host-Guest Docking

Keyword

Description
-dock GUEST [GUEST ...]

Determine best binding position of a single or
multiple guests to a host system. GUEST is xyzfile
with one or more guests. Multiple xyzfile can be
specified, by separating them with spaces. The charge
and multiplicity are of each invidual guest is read
from the comment line of the entry in the xyzfile(s).
Therefore, the comment line must contain exactly two
integers, where the first is the charge and second one
the multiplicity.
-no-dock
Disable docking procedure.
-dock-only GUEST [GUEST ...]

This keyword has the same function as '-dock', but it
also turns off any other workflow.
-dock-nrepeat N
Add guest(s) N times in docking process. Guests are
read repeated in the order the order they were read.
-dock-guest-charge DOCK_GUEST_CHARGE

Set the total charge for every guest structure. By
default the charge is read from the first column of
the XYZ comment line (if present).
-dock-guest-mult DOCK_GUEST_MULT

Set multiplicity for every guest structure. By default
the multiplicity is read from the second column of the
XYZ comment line (if present).
-dock-level {normal,quick,screening,complete}

Level of sophistication used for docking.
-dock-bondfactor N
Bonding factor N (e.g 1.5), by which the sum of the
radii of host and guest is scaled. If the
intermolecular distance is below this value, host and
guest are considered to be bound.
-dock-fixhost
Keep the geometry of the host fixed during docking.
-dock-no-fixhost
Do not keep the geometry of the host fixed during
docking.

Bee

Keyword

Description
-bee-workflow ID
Load workflow from Bee in order to update.
-bee-conf ID [ID ...]

Load list of conformers from Bee.

Conformational Entropy

Keyword

Description
-ensemblethermo
Compute the conformational entropy of the
energetically lowest conformer.
-no-ensemblethermo
Do not compute the conformational entropy of the
energetically lowest conformer.

Remove Duplicates

Keyword

Description
-rmduplicates
Remove duplicate structures. Checks are done after
reading the input structure, the pre-optimization, and
the optimization.