Solvation Keywords in the Jaguar Input File

Overview
Examples

Jaguar provides four continuum solvation models, PBF, SM6/SM8, SMD, and PCM. The solvation keywords that apply to all models or to more than one model are described in Table 1. By default, Jaguar calculations are performed in the gas phase, so isolv=0 and all other solvation keywords are irrelevant. Keywords for each of the solvation models are given in the sections below.

For solvated geometry optimizations, the trust keyword, which is described in Geometry Optimization and Transition-State Keywords in the Jaguar Input File, has a default value of 0.1 instead of its usual default of 0.3.

Note: QSite does not support continuum solvation, so you cannot add these keywords to a QSite input file.

Table 1. General keywords for solvation calculations
Keyword	Value	Description
isolv	0	Do not perform a solvation calculation.
	2	Perform a solvation calculation using a Poisson-Boltzmann solver [15, 222]
	5	Perform a solvation calculation using the SM6 model [231], which applies only to water. This is the only solvation keyword that should be specified when performing SM6 calculations. Only available for single-point calculations.
	6	Perform a solvation calculation using the SM8 model [223]. Can be used with the solvent keyword for any of the recognized solvents; other keywords are not relevant. Only available for single-point calculations.
	7	Perform a solvation calculation using the polarizable continuum model (PCM). The specific variant of the model is set with the pcm_model keyword.
	8	Perform a solvation calculation using the SMD model [321]. Can be used with the solvent keyword for any of the recognized solvents; other keywords are not relevant. The SMD solvent model is similar to SM8 with a re-fit non-electrostatic contribution to the free energy and the use of CPCM for the electrostatic contribution (rather than generalized Born like in SM8).
solvent_model	gas vacuum pbf sm6 sm8 pcm smd	Sets isolv = 0 Sets isolv = 0 Sets isolv= 2 Sets isolv = 5 Sets isolv = 6 Sets isolv = 7 Sets isolv = 8
solvent	water	Solvent name. The allowed values are listed below.
solvation_entropy	0	The ideal gas entropy approximation is used for the calculation of the entropy and total free energy.
	1	Garza's S_ω entropy approximation is used for the calculation of the entropy and total free energy. See Solvation Entropy in Jaguar.
	2	Garza's S_ε entropy approximation is used for the calculation of the entropy and total free energy. See Solvation Entropy in Jaguar.
	3	Garza's S_εα entropy approximation is used for the calculation of the entropy and total free energy. See Solvation Entropy in Jaguar.
pbf_after_pcm	0	Do not run a single-point PBF calculation after optimization with PCM solvation.
	1	Run a single-point PBF calculation after optimization with PCM solvation.
pbf_after_smd	0	Do not run a single-point PBF calculation after optimization with SMD solvation.
	1	Run a single-point PBF calculation after optimization with SMD solvation.
epsout	80.37	Dielectric constant of solvent. Used for PBF, PCM, and SM8 models.
sconv	1.5×10⁻⁴	Solvation energy convergence criterion in Hartrees
esolv0	number	Gas phase energy of molecule, in Hartrees; used in some restart (new input) files for solvation jobs

Available Solvents

The solvents available for use with the solvent keyword with the PBF, PCM, and SM8 models are listed below. Solvents are defined by their dielectric constant and their optical dielectric constant.

1,1,1-trichloroethane	acetonitrile	fluorobenzene
1,1,2-trichloroethane	acetophenone	formamide
1,2,4-trimethylbenzene	aniline	formic_acid
1,2-dibromoethane	anisole	n-heptane
1,2-dichloroethane	benzaldehyde	n-hexadecane
1,2-ethanediol	benzene	n-hexane
1,4-dioxane	benzonitrile	hexanoic_acid
1-bromo-2-methylpropane	benzyl_alcohol	iodobenzene
1-bromooctane	bromobenzene	iodoethane
1-bromopentane	bromoethane	iodomethane
1-bromopropane	bromoform	isopropylbenzene
1-butanol	butanal	p-isopropyltoluene
1-chlorohexane	butanoic_acid	mesitylene
1-chloropentane	butanone	methanol
1-chloropropane	butanonitrile	methyl_benzoate
1-decanol	butyl_ethanoate	methyl_butanoate
1-fluorooctane	butylamine	methyl_ethanoate
1-heptanol	n-butylbenzene	methyl_methanoate
1-hexanol	sec-butylbenzene	methyl_propanoate
1-hexene	tert-butylbenzene	N-methylaniline
1-hexyne	carbon_disulfide	methylcyclohexane
1-iodobutane	carbon_tetrachloride	N-methylformamide_(E/Z_mixture)
1-iodohexadecane	chlorobenzene	nitrobenzene
1-iodopentane	chloroform	nitroethane
1-iodopropane	a-chlorotoluene	nitromethane
1-nitropropane	o-chlorotoluene	o-nitrotoluene
1-nonanol	m-cresol	n-nonane
1-octanol	o-cresol	n-octane
1-pentanol	cyclohexane	n-pentadecane
1-pentene	cyclohexanone	pentanal
1-pentyne	cyclopentane	n-pentane
1-propanol	cyclopentanol	pentanoic_acid
2,2,2-trifluoroethanol	cyclopentanone	pentyl_ethanoate
2,2,4-trimethylpentane	decalin_(cis/trans_mixture)	pentylamine
2,4-dimethylpentane	cis-decalin	perfluorobenzene
2,4-dimethylpyridine	n-decane	propanal
2,6-dimethylpyridine	dibromomethane	propanoic_acid
2-bromopropane	dibutyl_ether	propanonitrile
2-butanol	o-dichlorobenzene	propyl_ethanoate
2-chlorobutane	E-1,2-dichloroethene	propylamine
2-heptanone	Z-1,2-dichloroethene	pyrrolidine
2-hexanone	dichloromethane	pyridine
2-methoxyethanol	diethyl_ether	tetrachloroethene
2-methyl-1-propanol	diethyl_sulfide	tetrahydrofuran
2-methyl-2-propanol	diethylamine	tetrahydrothiophene-S,S-dioxide
2-methylpentane	diiodomethane	tetralin
2-methylpyridine	diisopropyl_ether	thiophene
2-nitropropane	cis-1,2-dimethylcyclohexane	thiophenol
2-octanone	dimethyl_disulfide	toluene
2-pentanone	N,N-dimethylacetamide	trans-decalin
2-propanol	N,N-dimethylformamide	tributyl_phosphate
2-propen-1-ol	dimethylsulfoxide	trichloroethene
E-2-pentene	diphenyl_ether	triethylamine
3-methylpyridine	dipropylamine	n-undecane
3-pentanone	n-dodecane	water
4-heptanone	ethanethiol	xylene_(mixture)
4-methyl-2-pentanone	ethanol	m-xylene
4-methylpyridine	ethyl_ethanoate	o-xylene
5-nonanone	ethyl_methanoate	p-xylene
acetic_acid	ethyl_phenyl_ether
acetone	ethylbenzene

PBF Model

Most of the PBF solvation keywords correspond to GUI options described in Jaguar Solvation Settings. The keywords for the PBF model are described in Table 2. Defaults for some of these keywords are not indicated in bold italics, since the keywords’ default values generally depend on other keywords. The default values for the real-valued parameters are for water. The solvent can be specified with the solvent keyword. For a custom solvent, you can specify the dielectric constant and probe radius; the solvent keyword sets these two quantities as described below.

Water’s probe radius is set to 1.40 to reproduce solvation energies properly. All other probe radii are calculated from r³ = (3mΔ)/(4πρ) (10²⁴Å³/cm³), where r is the solvent probe radius in angstroms, m is the molecular mass obtained by dividing the molecular weight given in Ref. [104] in g mol⁻¹ by 6.02 x 10²³, Δ is the packing density, and ρ is the density in g/cm³ at 20°C obtained from ref. [104]. Finding the actual Δ would require a detailed knowledge of the structure of the liquid. Currently, all Δ values for these liquids are assumed to be 0.5. (For FCC lattices, Δ is 0.7405, and for BCC lattices, Δ is 0.6802.)

If you use water as the solvent, you have the choice of two methods of defining the cavity. The default is to use the van der Waals radii, as defined in the pbf_radii.ark file (or in the old default.lewis file, if pbf_radii=0). The alternative is to use an isosurface of the density: that is, the cavity is the surface at a specified, small value of the electron density. To use this method, set pbf_isodens=1. This method removes the need to define fixed van der Waals radii for each atom type, and automatically adjusts to changes in the electron density (as a real solvent would). It includes an explicit solvent correction factor based on the assumption that the interaction with the solvent is a function of the electric field on the molecular surface [272]. When you use this method, you should include diffuse functions in the basis set, which are important for polar groups and for anions. This method is particularly recommended for computing the solvation energy of anions.

Note: The explicit correction is known to overestimate the interaction with the solvent for systems containing nitro groups or multiple fluorine atoms.

Several keywords are available for the control of the finite-element mesh used by the Poisson-Boltzmann solver. To increase the resolution, you can increase the values of pbf_nshells, pbf_molsurf_idx, pbf_protosph_res, and pbf_boundary_res and decrease the values of pbf_fem_mxres_cg.

Table 2. Keywords for PBF solvation calculations
Keyword	Value	Description
icavity	0	Do not include solute cavity energy term in solvation calculation
	1	Include solute cavity energy term for water, do not include it for other solvents
	2	Force calculation of cavity energy term for all solvents
isurf	0	Do not include the first shell correction factor term in the solvation energy
	1	Include the first shell correction factor term in the solvation energy (default for most calculations in water; turns on ivanset=1 by default). Ignored if pbf_isodens=1 or icavity = 0 or the solvent is not water.
	2	Force calculation of first shell correction factor term for all solvents. Ignored if icavity = 0 or if the solvent is not water and icavity=1.
ivanset	0	Do not set van der Waals radii according to Lewis structure
	1	Set van der Waals radii according to the Lewis structure specified by lewstr (1 by default); see LMP2 Keywords in the Jaguar Input File. Only used if pbf_isodens=0 and pbf_radii=0.
kesep	0	Combine terms for all one-electron matrices
	1	Keep kinetic energy terms, nuclear attraction integrals, and point charge terms separate (Note: if isolv=2, kesep=1 by default)
isolvg	0	Compute gradients in solvent with method used in Jaguar 3.5 and earlier.
	1	Compute gradients in solvent with robust Jaguar 4.0 method.
	2	Compute gradients in solvent with improved Jaguar 7.8 method.
pbf_nshells	9	Number of shells around each atom in the finite-element mesh.
pbf_molsurf_idx	4	The index of the shell to use for the molecular surface.
pbf_protosph_res	21	The Lebedev angular scheme (see Table 1) on the prototype atomic sphere.
pbf_boundary_res	14	The Lebedev angular scheme (see Table 1) at the dielectric boundary.
pbf_fem_mxres_cg	10⁻⁴	The maximum residual for the charge scaling solver.
pbf_isodens	0	Do not use the density isosurface to construct the PBF grid.
	1	Use the density isosurface to construct the PBF grid, rather than using preset van der Waals radii. This method is not available with ECPs, and can only be used for water. If you set this keyword, pbf_radii, ivanset, and isurf are ignored.
pbf_molsurf_iso	0.001	Value of the density for the isosurface.
pbf_boundary_iso	10⁻⁵⁰	Value of the isodensity on the molecular boundary.
pbf_radii	0	Use the `default.lewis` file to define the van der Waals radii.
	1	Use the `pbf_radii.ark` file to define the van der Waals radii, and determine the connectivity from the Maestro file.
	2	Use the `pbf_radii.ark` file to define the van der Waals radii, and determine the connectivity from the coordinates in the Jaguar input file.
	4	Use the LAD-PBF method to define the van der Waals radii. The radii are adjusted for each molecule in a scheme similar to that described in the work of Plett et al.
res_inner	8.0	Factor controlling the resolution of the inner surfaces.
res_outer	16.0	Factor controlling the resolution of the outer surfaces, excluding boundary.
res_boundary	0.2	Resolution on the boundary shell.
res_molsurf	2.2	Resolution on the molecular surface.
isotrymax	30	Maximum number of attempts to reduce an inner density that is too large.
epsin	1.0	Inner dielectric constant of solvent [252]
radprb	1.40	Radius of solvent probe molecule
maxpbfit	100	Maximum number of PBF solvation iterations.

SM8 model

Additional solvents for SM8 can be specified by means of several descriptors, for which the keywords are listed in Table 3. To use a custom solvent, the dielectric constant, index of refraction, acidity and basicity can be derived from experiment, or from interpolation or extrapolation of data available for other solvents, and the fraction of aromatic and halogen atoms can be computed from the chemical formula of the solvent. Solvent parameters for common organic solvents are tabulated in the Minnesota Solvent Descriptor Database, available at: http://comp.chem.umn.edu/solvation/mnsddb.pdf.

Table 3. Keywords for SM8 custom solvents
Keyword	Description
epsout	Dielectric constant ε
sm8_sola	Abraham’s hydrogen bond acidity α, also called Σα₂^H
sm8_solb	Abraham’s hydrogen bond acidity β, also called Σβ₂^H
sm8_solc	Aromaticity: the fraction of non-hydrogen solvent atoms that are aromatic carbon atoms
sm8_solg	Macroscopic surface tension at the air/solvent interface at 298 K, in cal mol⁻¹ Å⁻²
sm8_solh	Electronegative halogenicity: fraction of non-hydrogen solvent atoms that are F, Cl, Br
sm8_soln	index of refraction at optical frequencies at 293 K, n ≡ n₂₀D

PCM Model

The polarizable continuum models (PCM) use a molecule-shaped cavity and the full molecular electrostatic potential to obtain apparent surface charge. They include the conductor-like screening models, COSMO [232], GCOSMO [233], and C-PCM [234], and the surface simulation of volume polarization for electrostatics (SS(v)PE [235], which is also known as the "integral equation formalism" (IEF-PCM) [236, 237]. The COSMO and C-PCM models are closely related: the only difference between them comes from a dielectric charge screening factor in the form

−(ε_solv − 1.0) / (ε_solv + s)

where ε_solv is the solvent dielectric constant (set by keyword epsout) or the solvent optical dielectric constant, for TDDFT calculations (set by keyword epsout_opt); and s is the dielectric charge screening factor, set by the keyword pcm_dcs, with the value 0.5 in the COSMO model and 0.0 in the C-PCM model.

The cavity surface is a crucial aspect of PCMs, and the computed properties are quite sensitive to the details of the cavity construction. In Jaguar, the PCM cavity surface is discretized using atom-centered Lebedev grids with specified atomic radii, set with the keywords pcm_vdwscale and pcm_radii. The number of grid points distributed on the sphere surface can be set with the keywords pcm_lebedev_hatom and pcm_lebedev_heavy. Grid points can be discarded if their switching function is less than a threshold, defined by the pcm_switch_thresh keyword.

The discretization procedure usually generates discontinuous potential energy surfaces when the solute system is updated. This is because the surface grid points may emerge from, or disappear within, the solute cavity as the atomic spheres that define the cavity are moved. This can make geometry optimizations very difficult to converge, and produce large errors in vibrational frequency calculations. Jaguar uses smoothing schemes to overcome the problems of the discontinuous potential energy surface, following either the work of Lange and Herbert [238, 239], or the work of York and Karplus [240]. The smoothing scheme can be selected with the keyword pcm_smooth_method.

For the COSMO model, Jaguar can store the screening charge surface in a .cosmo file that can be used as input for the COSMOTherm program. Set iwrt_cosmo=1 to write a COSMOTherm input file. COSMOTherm is not part of the software installation and is not distributed by Schrödinger.

Table 4. Keywords for PCM solvation calculations.
Keyword	Value	Description
epsout_opt	real	Solvent optical dielectric constant, used for TDDFT calculations (square of refractive index)
pcm_model	`cosmo`	Use the COSMO model [232].
	`cpcm`	Use the C-PCM model [234].
	`ssvpe`	Use the SS(v)PE model [235].
pcm_dcs	real	Dielectric charge screening factor. The value is 0.5 in the COSMO model, 0.0 in the C-PCM model.
pcm_vdwscale	1.2	Van der Waals radius scaling factor, used to define the cavity surface.
pcm_radii	`bondi`	Use Bondi (van der Waals) atomic radii [241], multiplied by the van der Waals radius scaling factor, pcm_vdwscale.
	`uff`	Use Universal Force Field (UFF) atomic radii [105].
	`klamt`	Use Klamt atomic radii [242].
	`draco`	Use the DRACO scaled Bondi atomic radii [328]. Only available for solvent_model=pcm (pcm_model= cpcm or cosmo) and solvent_model=smd (pcm_model=cpcm).
pcm_lebedev_hatom	86	Number of Lebedev grid points for H atoms.
pcm_lebedev_heavy	146	Number of Lebedev grid points for non-H (heavy) atoms.
pcm_switch_thresh	10⁻⁸	Threshold for discarding grid points based on their switching function.
pcm_smooth_method	`lh`	Use the smoothing method of Lange and Herbert [238, 239].
	`yk`	Use the smoothing method of York and Karplus [240].
iwrt_cosmo	0	Do not write a COSMOTherm input file
	1	Write a COSMOTherm input file

Solvation entropy keywords

To calculate solvation entropy with a custom solvent, set the keyword solvent=other in the gen section of the Jaguar input file. You must then supply the following parameters for the solvent:

Table 5. Keywords for solvation entropy
Keyword	Description
garza_solvent_acentric_factor	Pitzer acentric factor ω. Needed for S_ω. Available by default for some solvents.
garza_solvent_dielectric	Dielectric constant ε. Needed for S_ϵ and S_ϵα. Available by default for all defined solvents.
garza_solvent_expansion_coeff	Thermal expansion coefficient α. Needed for S_ϵα. Available by default for some solvents.
garza_solvent_mol_weight	Molecular weight, in g/mol.
garza_solvent_density	Density, in g/mL.
garza_solvent_volume	Volume of a single solvent molecule, in ang³.
garza_solvent_surface_area	Surface area of a single solvent molecule, in ang².
garza_solvent_rad_of_gyration	Radius of gyration of a single solvent molecule, in ang.

Single Point Energy Examples

Vibrational Frequency Examples

Geometry Optimization Examples

Calculation of Molecular Properties Examples

Excited State Calculation Examples

Workflow Examples

Example: Generation of conformers and tautomers in water solvent with the AutoConf.py workflow

Note: Use PM3 tautomer filtering in solution phase, B3LYP-D3/LACVP** geometry optimization with PCM implicit solvation method in water, and M06-2X/cc-pVTZ(-f) final single point energy calculation with PBF implicit solvation method in water. When using the PCM solvation method (set by isolv: 7) it is important to also set the following settings: stop_rxn: 0, check_min: 0, effectively disabling the settings stop_rxn and check_min, because they currently don't work with PCM.

Example input file (wflow-confgen_solv-0001-config.in):

TautomerStage:
    backend_options:
        disable_fast_pka: True
        active_atoms: [2]
        charge: 0

SemiEmpStage1:
    nkeep: 100
    erg_window: 100.0
    backend_options:
        method: PM3
        nogeopt: True
        energy_only: True
        keywords: 'GEO-OK NOREOR SCFCRT=1.0 ITRY=200 PL T=30D'

ConformerStage:
    erg_window: 100000.0
    backend_options:
        max_conf: 5
        erg_window: 50.0
        acc_level: std
        do_gas_csrch: False

SemiEmpStage2:
    nkeep: 100
    erg_window: 100.0
    backend_options:
        method: PM3
        nogeopt: True
        energy_only: True
        keywords: 'GEO-OK NOREOR SCFCRT=1.0 ITRY=200 PL T=30D'

QMStage1:
    nkeep: 25
    erg_window: 50.0
    canonical: True
    backend_options:
        basis: LACVP**
        dftname: B3LYP-D3
        igeopt: 1
        nofail: 0
        stop_rxn: 0
        check_min: 0
        isolv: 7
        nogas: 2
        solvent: water

QMStage2:
    nkeep: 5
    canonical: True
    backend_options:
        basis: cc-pVTZ(-f)
        dftname: M06-2X
        nofail: 1
        isolv: 2
        nogas: 2
        solvent: water

Example input structure file (wflow-confgen_solv-0001.mae):

{
 s_m_m2io_version
 :::
 2.0.0
}

f_m_ct {
 s_m_title
 s_m_entry_id
  s_m_entry_name
  i_m_ct_format
  :::
  Heterocycle
   3
   entry
   2
  m_atom[10] {
   # First column is atom index #
   i_m_mmod_type
   r_m_x_coord
   r_m_y_coord
   r_m_z_coord
   i_m_color
   i_m_atomic_number
   s_m_color_rgb
   i_rdk_index
   :::
   1 25 -1.982786 0.714835 0.000001 43 7 5757FF  0
   2 2 -2.113989 -0.648817 -0.000000 2 6 A0A0A0  1
   3 2 -0.818862 -1.133755 0.000000 2 6 A0A0A0  2
   4 2 0.000000 0.000000 0.000000 2 6 A0A0A0  3
   5 25 -0.699477 1.113590 0.000000 43 7 5757FF  4
   6 16 1.380000 0.000000 0.000000 70 8 FF2F2F  5
   7 43 -2.765439 1.368660 0.000004 21 1 FFFFFF  <>
   8 41 -3.085971 -1.126690 0.000002 21 1 FFFFFF  <>
   9 41 -0.503348 -2.169136 -0.000000 21 1 FFFFFF  <>
   10 42 1.802618 -0.906308 -0.000000 21 1 FFFFFF  <>
   :::
  }
  m_bond[10] {
   # First column is bond index #
   i_m_from
   i_m_to
   i_m_order
   :::
   1 1 2 1
   2 1 5 1
   3 1 7 1
   4 2 3 2
   5 2 8 1
   6 3 4 1
   7 3 9 1
   8 4 5 2
   9 4 6 1
   10 6 10 1
   :::
  }
 }

To submit the job from the command line, download the input files (below) and enter the following command:

$SCHRODINGER/jaguar run AutoConf.py -config wflow-confgen_solv-0001-config.in wflow-confgen_solv-0001.mae -jobname wflow_confgen_solv_0001

Click a button to download the file. The Output files are those produced when the job is run.

Files generated with release version: 2024-4

Input file: wflow-confgen_solv-0001-config.in

Input structure: wflow-confgen_solv-0001.mae

Output files

Example: Execute solvation.py workflow to calculate water/1-octanol (1) logD and logP partition coefficients and (2) solvation energies for benzenethiol. The benzenethiol pKa is predicted by the program Epik. SM8 solvation model used. Conformers generated by a conformation search are optimized in both solvent phases

Note: To calculate LogD, we examine pHs of 6.2, 7.4, and 8.2 since the pKa for thiol deprotenation is estimated to be 6.49. Macro-pKa can also be used for pKa prediction for complicated systems.

Example input file (wflow-solvation-0001.in):

input = wflow-solvation-0001.mae
phase1 = water
phase2 = 1-octanol
logP = True
logD = True
solvation_method = SM8
pka_method = epikx
pHs = [6.2, 7.4, 8.2]
&JaguarKeywords
basis = 6-31G**
dftname = M06-2X
maxitg = 200
isymm = 0
maxit = 400
&

Example input structure file (wflow-solvation-0001.mae):

{ 
 s_m_m2io_version
 :::
 2.0.0 
} 

f_m_ct { 
 s_m_title
 i_m_ct_enhanced_stereo_status
 s_m_entry_id
 s_m_entry_name
 b_sd_chiral_flag
 i_sd_version
 s_m_Source_Path
 s_m_Source_File
 i_m_Source_File_Index
 i_m_ct_format
 :::
 Structure1 
  0
  1 
  benz.1 
  0
  0
  /Users/moore1 
  benz.xyz 
  1
  2
 m_atom[13] { 
  # First column is atom index #
  i_m_mmod_type
  r_m_x_coord
  r_m_y_coord
  r_m_z_coord
  i_m_residue_number
  i_m_color
  i_m_atomic_number
  s_m_color_rgb
  :::
  1 2 -2.797800 0.001100 0.126500 900 2 6 A0A0A0 
  2 2 -2.080600 1.198400 0.133000 900 2 6 A0A0A0 
  3 2 -0.686900 1.190000 0.162400 900 2 6 A0A0A0 
  4 2 0.006000 -0.027900 0.185600 900 2 6 A0A0A0 
  5 2 -0.712200 -1.230300 0.179000 900 2 6 A0A0A0 
  6 2 -2.106100 -1.210400 0.149700 900 2 6 A0A0A0 
  7 49 1.795300 0.024700 0.222300 900 13 16 E1E11E 
  8 41 -3.883100 0.011800 0.103500 900 21 1 FFFFFF 
  9 41 -2.607000 2.148500 0.115100 900 21 1 FFFFFF 
  10 41 -0.140500 2.128700 0.167200 900 21 1 FFFFFF 
  11 41 -0.187500 -2.181000 0.196400 900 21 1 FFFFFF 
  12 41 -2.650900 -2.150100 0.144800 900 21 1 FFFFFF 
  13 41 1.997400 -1.306600 0.238400 900 21 1 FFFFFF 
  :::
 } 
 m_bond[13] { 
  # First column is bond index #
  i_m_from
  i_m_to
  i_m_order
  :::
  1 1 2 2
  2 1 6 1
  3 1 8 1
  4 2 3 1
  5 2 9 1
  6 3 10 1
  7 3 4 2
  8 4 7 1
  9 4 5 1
  10 5 11 1
  11 5 6 2
  12 6 12 1
  13 7 13 1
  :::
 } 
}

To submit the job from the command line, download the input files (below) and enter the following command:

$SCHRODINGER/jaguar run solvation.py -jobname=wflow_solvation_0001 wflow-solvation-0001.in

Click a button to download the file. The Output files are those produced when the job is run.

Files generated with release version: 2024-4

Input file: wflow-solvation-0001.in

Input structure: wflow-solvation-0001.mae

Output files