External Methods Keywords in the Jaguar Input File (Machine learning methods and xTB)

  • Overview
  • Examples

Table 1 lists the keywords that are related to using machine learning methods with Jaguar calculations. Table 2 lists keywords that are related to using xTB with Jaguar calculations.

Table 1. Machine learning keywords

Keyword

Value

Description

ani

0

Calculate energy and derivatives quantum-mechanically.

 

1

Calculate energy and derivatives with the Schrodinger-ANI neural-network potential energy surface, derived from fitting to QM calculations for a large set of drug-like molecules [294]. This surface is only available for the elements H, C, N, O, F, P, S, and Cl. As this is essentially a force-field calculation, setting this keyword only permits geometry optimizations and calculation of frequencies.

 

2

Calculate energy and derivatives with the ANI-1ccx neural-network potential energy surface, derived from fitting to DFT and CCSD(T) calculations for a large set of drug-like molecules [293]. This surface is only available for the elements H, C, N, O. As this is essentially a force-field calculation, setting this keyword only permits geometry optimizations and calculation of frequencies.

qrnn

0

Calculate energy and derivatives quantum-mechanically.

 

1

Calculate energy and derivatives with the direct-learned QRNN (charge recursive neural-network) potential energy surface, derived from fitting to DFT calculations for a large set of ionic drug-like molecules and their tautomers [303].
This surface is only available for the elements H, C, N, O, F, P, S, and Cl. This surface cannot be applied to open-shell systems. As this is essentially a force-field calculation, setting this keyword only permits geometry optimizations and calculation of frequencies.

 

2

Calculate energy and derivatives with the delta-learned QRNN (charge recursive neural-network) potential energy surface, derived from fitting to the difference between QM and DFT calculations for a large set of ionic drug-like molecules and their tautomers [303].
This surface is only available for the elements H, C, N, O, F, P, S, and Cl. This surface cannot be applied to open-shell systems. As this is essentially a force-field calculation, setting this keyword only permits geometry optimizations and calculation of frequencies.

 

3

Calculate energy and derivatives with the delta-learned QRNN (charge recursive neural-network) + transfer-learning potential energy surface, derived from fitting to the difference between QM and DFT calculations for a large set of ionic drug-like molecules and their tautomers.
This surface is only available for the elements H, C, N, O, F, P, S, and Cl. This surface cannot be applied to open-shell systems. As this is essentially a force-field calculation, setting this keyword only permits geometry optimizations and calculation of frequencies.

 

4

Calculate energy and derivatives with the direct-learned QRNN (charge recursive neural-network) + transfer-learning potential energy surface, derived from fitting to the difference between QM and DFT calculations for a large set of ionic drug-like molecules and their tautomers.
This surface is only available for the elements H, C, N, O, F, P, S, and Cl. This surface cannot be applied to open-shell systems. As this is essentially a force-field calculation, setting this keyword only permits geometry optimizations and calculation of frequencies.

qrnn_solv

0

Do not add implicit solvation to the QRNN calculations.

 

1

Add implicit solvation to QRNN calculations. This setting only works if qrnn is set to 2 or 3. Select the solvent model with qrnn_solvent_model and the solvent with solvent.

qrnn_solvent_model

ALPB

Use the analytic linearized Poisson–Boltzmann (ALPB) solvent model when implicit solvation is enabled [313].

 

GBSA

Use the Generalized Born and surface area (GBSA) solvent model [325].

 

COSMO

Use the Conductor-like Screening Model (COSMO) solvent model[232].

 

CPCMX

Use the Extended Conductor-like Polarizable Continuum Model (CPCM-X) solvent model. Note: only single point energy calculations can be performed with this model as first and second derivatives are not available [326].

mlff

Any

Calculate energy and derivatives with a machine learning force field (MLFF). For MPNICE (Message Passing Network with Iterative Charge Equilibration) machine learning force fields, the keyword value can be any model listed in this table. This method cannot be applied to open-shell systems. As this is essentially a force-field calculation, setting this keyword only permits geometry optimizations and calculation of frequencies.

You can also use the UMA model, specified by the UMA_sm_omol keyword value.

mlff_solv

0

Do not add implicit solvation to the MPNICE calculations.

 

1

Add implicit solvation to MPNICE calculations. This setting only works if mlff is set to Organic_MPNICE_TB. Select the solvent model with mlff_solvent_model and the solvent with solvent.

mlff_solvent_model

ALPB

Use the analytic linearized Poisson–Boltzmann (ALPB) solvent model when implicit solvation is enabled [313].

 

GBSA

Use the Generalized Born and surface area (GBSA) solvent model [325].

 

COSMO

Use the Conductor-like Screening Model (COSMO) solvent model[232].

 

CPCMX

Use the Extended Conductor-like Polarizable Continuum Model (CPCM-X) solvent model. Note: only single point energy calculations can be performed with this model as first and second derivatives are not available [326].

solvent

water

Solvent name. The allowed values are listed below.

mlff_use_pbc

0

All inputs are treated as a molecular system even if periodic boundary condition (PBC) information is found.

 

1

Attempt to find periodic boundary condition (PBC) information in the input .mae and pass it along to MLFF calculations. If no PBC information is found, the calculation continues on as a molecular calculation. PBC information can come in two forms (listed in order of precedence if both are available):

  1. The 9 Maestro properties r_chorus_box_(ax, ay, az, bx, by, bz, cx, cy, cz), where the properties are the x,y,z components of the 3 cell vectors in Angstroms.

  2. The 6 Maestro properties r_pdb_PDB_CRYST1_(a, b, c, alpha, beta, gamma), where the properties are the lengths of the cell vectors (Angstroms) and the angles between them (Degrees). alpha=between b and c, beta= between a and c, gamma=between a and b.

 

2

Attempt to find periodic boundary condition (PBC) information in the input .mae and pass it along to MLFF calculations. If no PBC information is found, the calculation stops. PBC information can come in two forms (listed in order of precedence if both are available):

  1. The 9 Maestro properties r_chorus_box_(ax, ay, az, bx, by, bz, cx, cy, cz), where the properties are the x,y,z components of the 3 cell vectors in Angstroms.

  2. The 6 Maestro properties r_pdb_PDB_CRYST1_(a, b, c, alpha, beta, gamma), where the properties are the lengths of the cell vectors (Angstroms) and the angles between them (Degrees). alpha=between b and c, beta= between a and c, gamma=between a and b.

Table 2. xTB keywords.

Keyword

Value

Description

xtb

0

Calculate energy and derivatives quantum-mechanically.

 

1

Calculate energy and derivatives with the GFN2-xTB semiempirical method [327].

xtb_solv

0

Do not add implicit solvation to xTB calculations.

 

1

Add implicit solvation to xTB calculations. This setting only works if xtb is set to 1. Select the solvent model with xtb_solvent_model and the solvent with solvent.

xtb_solvent_model

ALPB

Use the analytic linearized Poisson–Boltzmann (ALPB) solvent model when implicit solvation is enabled [313].

 

GBSA

Use the Generalized Born and surface area (GBSA) solvent model [325].

 

COSMO

Use the Conductor-like Screening Model (COSMO) solvent model[232].

 

CPCMX

Use the Extended Conductor-like Polarizable Continuum Model (CPCM-X) solvent model. Note: only single point energy calculations can be performed with this model as first and second derivatives are not available [326].

solvent

water

Solvent name. The allowed values are listed below.

Available Solvents

The solvents available for use with the solvent keyword with the ALPB, COSMO, and CPCMX models are listed below.

acetonitrile

aniline

benzene

dichloromethane

chloroform

carbon_disulfide

N,N-dimethylformamide

dimethylsulfoxide

diethyl_ether

ethanol

ethyl_ethanoate

n-hexadecane

n-hexane

nitromethane

1-octanol

toluene

tetrahydrofuran

Single Point Energy Examples

Note: A faster, but potentially less, accurate QRNN model can be run by using `qrnn=4`.

Example input file (ene-qrnn-0001.in):

&gen
qrnn=3
&
&zmat
C1     -1.5933590000000  -1.0264000000000  -2.1954570000000
C2     -0.5656280000000  -0.4807620000000  -1.2027750000000
H3     -1.5602110000000  -0.4934300000000  -3.1469390000000
H4     -2.6061140000000  -0.9442130000000  -1.7994750000000
H5     -1.4133670000000  -2.0815530000000  -2.4040480000000
H6     -0.5883360000000  -1.0257360000000  -0.2566760000000
N7      0.7496070000000  -0.5200290000000  -1.7798490000000
O8     -0.7722320000000   0.8823370000000  -0.9690390000000
H9     -1.5254740000000   1.1673140000000  -1.4657350000000
H10     1.3540870000000   0.0547150000000  -1.2090720000000
H11     1.1215960000000  -1.4577370000000  -1.7356190000000
&

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

$SCHRODINGER/jaguar run -jobname=ene_qrnn_0001 ene-qrnn-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: ene-qrnn-0001.in
Output files

Note: Only water implicit solvent is available. Solvent model is not available for neither `qrnn=1` nor `qrnn=4`.

Example input file (ene-qrnn_solv-0001.in):

&gen
qrnn=3
qrnn_solv=1
&
&zmat
C1     -1.5933590000000  -1.0264000000000  -2.1954570000000
C2     -0.5656280000000  -0.4807620000000  -1.2027750000000
H3     -1.5602110000000  -0.4934300000000  -3.1469390000000
H4     -2.6061140000000  -0.9442130000000  -1.7994750000000
H5     -1.4133670000000  -2.0815530000000  -2.4040480000000
H6     -0.5883360000000  -1.0257360000000  -0.2566760000000
N7      0.7496070000000  -0.5200290000000  -1.7798490000000
O8     -0.7722320000000   0.8823370000000  -0.9690390000000
H9     -1.5254740000000   1.1673140000000  -1.4657350000000
H10     1.3540870000000   0.0547150000000  -1.2090720000000
H11     1.1215960000000  -1.4577370000000  -1.7356190000000
&

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

$SCHRODINGER/jaguar run -jobname=ene_qrnn_solv_0001 ene-qrnn_solv-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: ene-qrnn_solv-0001.in
Output files

Note: The charge and spin multiplicity are taken from the input .mae file in this example. They can also be specified by flags for the Schrodinger xTB wrapper. Multiple structures can be included in the input .mae file.

Example input structure file (ene-xtb-0001.mae):

{ 
 s_m_m2io_version
 :::
 2.0.0 
} 

f_m_ct { 
 s_m_title
 s_m_entry_id
 s_m_entry_name
 s_m_Source_Path
 s_m_Source_File
 i_m_Source_File_Index
 i_m_ct_format
 i_m_Molecular_charge 
 i_m_Spin_multiplicity
:::
 Structure1 
  2 
  Structure1 
  /Users/moore1/examples/wflow-spectroscopy_vcd-0001 
  wflow-spectroscopy_vcd-0001.maegz 
  1
  2
  0
  1
 m_atom[11] { 
  # 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
  s_m_atom_name
  i_m_minimize_atom_index
  :::
  1 3 -1.593359 -1.026400 -2.195457 1 24 6 808080  C1  1
  2 3 -0.565628 -0.480762 -1.202775 1 2 6 A0A0A0  C2  2
  3 41 -1.560211 -0.493430 -3.146939 1 21 1 FFFFFF  H3  3
  4 41 -2.606114 -0.944213 -1.799475 1 21 1 FFFFFF  H4  4
  5 41 -1.413367 -2.081553 -2.404048 1 21 1 FFFFFF  H5  5
  6 41 -0.588336 -1.025736 -0.256676 1 21 1 FFFFFF  H6  6
  7 26 0.749607 -0.520029 -1.779849 1 43 7 5757FF  N7  7
  8 16 -0.772232 0.882337 -0.969039 1 70 8 FF2F2F  O8  8
  9 42 -1.525474 1.167314 -1.465735 1 21 1 FFFFFF  H9  9
  10 43 1.354087 0.054715 -1.209072 1 21 1 FFFFFF  H10  10
  11 43 1.121596 -1.457737 -1.735619 1 21 1 FFFFFF  H11  11
  :::
 } 
 m_bond[10] { 
  # First column is bond index #
  i_m_from
  i_m_to
  i_m_order
  :::
  1 1 2 1
  2 1 3 1
  3 1 4 1
  4 1 5 1
  5 2 6 1
  6 2 7 1
  7 2 8 1
  8 7 10 1
  9 7 11 1
  10 8 9 1
  :::
 } 
}

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

$SCHRODINGER/xtb ene-xtb-0001.mae -jobname=ene_xtb_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 structure: ene-xtb-0001.mae
Output files

Note: The charge and spin multiplicity are taken from the input .mae file in this example. They can also be specified by flags for the Schrodinger xTB wrapper. Multiple structures can be included in the input .mae file.

Example input structure file (ene-xtb_solv-0001.mae):

{ 
 s_m_m2io_version
 :::
 2.0.0 
} 

f_m_ct { 
 s_m_title
 s_m_entry_id
 s_m_entry_name
 s_m_Source_Path
 s_m_Source_File
 i_m_Source_File_Index
 i_m_ct_format
 i_m_Molecular_charge 
 i_m_Spin_multiplicity
:::
 Structure1 
  2 
  Structure1 
  ene-xtb_solv-0001.mae
  ene-xtb_solv-0001.mae
  1
  2
  0
  1
 m_atom[11] { 
  # 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
  s_m_atom_name
  i_m_minimize_atom_index
  :::
  1 3 -1.593359 -1.026400 -2.195457 1 24 6 808080  C1  1
  2 3 -0.565628 -0.480762 -1.202775 1 2 6 A0A0A0  C2  2
  3 41 -1.560211 -0.493430 -3.146939 1 21 1 FFFFFF  H3  3
  4 41 -2.606114 -0.944213 -1.799475 1 21 1 FFFFFF  H4  4
  5 41 -1.413367 -2.081553 -2.404048 1 21 1 FFFFFF  H5  5
  6 41 -0.588336 -1.025736 -0.256676 1 21 1 FFFFFF  H6  6
  7 26 0.749607 -0.520029 -1.779849 1 43 7 5757FF  N7  7
  8 16 -0.772232 0.882337 -0.969039 1 70 8 FF2F2F  O8  8
  9 42 -1.525474 1.167314 -1.465735 1 21 1 FFFFFF  H9  9
  10 43 1.354087 0.054715 -1.209072 1 21 1 FFFFFF  H10  10
  11 43 1.121596 -1.457737 -1.735619 1 21 1 FFFFFF  H11  11
  :::
 } 
 m_bond[10] { 
  # First column is bond index #
  i_m_from
  i_m_to
  i_m_order
  :::
  1 1 2 1
  2 1 3 1
  3 1 4 1
  4 1 5 1
  5 2 6 1
  6 2 7 1
  7 2 8 1
  8 7 10 1
  9 7 11 1
  10 8 9 1
  :::
 } 
}

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

$SCHRODINGER/xtb ene-xtb_solv-0001.mae -solvation water -jobname=ene_xtb_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 structure: ene-xtb_solv-0001.mae
Output files

Geometry Optimization Examples

Note: With QRNN, all frequencies calculations are done numerically with finite-difference of gradients.

Example input file (opt_freq-qrnn-0001.in):

&gen
igeopt=1
ifreq=1
qrnn=3
qrnn_solv=1
&
&zmat
C1     -1.5933590000000  -1.0264000000000  -2.1954570000000
C2     -0.5656280000000  -0.4807620000000  -1.2027750000000
H3     -1.5602110000000  -0.4934300000000  -3.1469390000000
H4     -2.6061140000000  -0.9442130000000  -1.7994750000000
H5     -1.4133670000000  -2.0815530000000  -2.4040480000000
H6     -0.5883360000000  -1.0257360000000  -0.2566760000000
N7      0.7496070000000  -0.5200290000000  -1.7798490000000
O8     -0.7722320000000   0.8823370000000  -0.9690390000000
H9     -1.5254740000000   1.1673140000000  -1.4657350000000
H10     1.3540870000000   0.0547150000000  -1.2090720000000
H11     1.1215960000000  -1.4577370000000  -1.7356190000000
&

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

$SCHRODINGER/jaguar run -jobname=opt_freq_qrnn_0001 opt_freq-qrnn-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: opt_freq-qrnn-0001.in
Output files

Note: The charge and spin multiplicity are taken from the input .mae file in this example. They can also be specified by flags for the Schrodinger xTB wrapper. Multiple structures can be included in the input .mae file.

Example input structure file (opt-xtb-0001.mae):

{ 
 s_m_m2io_version
 :::
 2.0.0 
} 

f_m_ct { 
 s_m_title
 s_m_entry_id
 s_m_entry_name
 s_m_Source_Path
 s_m_Source_File
 i_m_Source_File_Index
 i_m_ct_format
 i_m_Molecular_charge 
 i_m_Spin_multiplicity
:::
 Structure1 
  2 
  Structure1 
  /Users/moore1/examples/wflow-spectroscopy_vcd-0001 
  wflow-spectroscopy_vcd-0001.maegz 
  1
  2
  0
  1
 m_atom[11] { 
  # 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
  s_m_atom_name
  i_m_minimize_atom_index
  :::
  1 3 -1.593359 -1.026400 -2.195457 1 24 6 808080  C1  1
  2 3 -0.565628 -0.480762 -1.202775 1 2 6 A0A0A0  C2  2
  3 41 -1.560211 -0.493430 -3.146939 1 21 1 FFFFFF  H3  3
  4 41 -2.606114 -0.944213 -1.799475 1 21 1 FFFFFF  H4  4
  5 41 -1.413367 -2.081553 -2.404048 1 21 1 FFFFFF  H5  5
  6 41 -0.588336 -1.025736 -0.256676 1 21 1 FFFFFF  H6  6
  7 26 0.749607 -0.520029 -1.779849 1 43 7 5757FF  N7  7
  8 16 -0.772232 0.882337 -0.969039 1 70 8 FF2F2F  O8  8
  9 42 -1.525474 1.167314 -1.465735 1 21 1 FFFFFF  H9  9
  10 43 1.354087 0.054715 -1.209072 1 21 1 FFFFFF  H10  10
  11 43 1.121596 -1.457737 -1.735619 1 21 1 FFFFFF  H11  11
  :::
 } 
 m_bond[10] { 
  # First column is bond index #
  i_m_from
  i_m_to
  i_m_order
  :::
  1 1 2 1
  2 1 3 1
  3 1 4 1
  4 1 5 1
  5 2 6 1
  6 2 7 1
  7 2 8 1
  8 7 10 1
  9 7 11 1
  10 8 9 1
  :::
 } 
}

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

$SCHRODINGER/xtb opt-xtb-0001.mae -optimize -jobname=opt_xtb_0001

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

Files generated with release version: 2025-4

Input structure: opt-xtb-0001.mae
Output files

Note: The charge and spin multiplicity are taken from the input .mae file in this example. They can also be specified by flags for the Schrodinger xTB wrapper. Multiple structures can be included in the input .mae file.

Example input structure file (opt-xtb_solv-0001.mae):

{ 
 s_m_m2io_version
 :::
 2.0.0 
} 

f_m_ct { 
 s_m_title
 s_m_entry_id
 s_m_entry_name
 s_m_Source_Path
 s_m_Source_File
 i_m_Source_File_Index
 i_m_ct_format
 i_m_Molecular_charge 
 i_m_Spin_multiplicity
:::
 Structure1 
  2 
  Structure1 
  /Users/moore1/examples/wflow-spectroscopy_vcd-0001 
  wflow-spectroscopy_vcd-0001.maegz 
  1
  2
  0
  1
 m_atom[11] { 
  # 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
  s_m_atom_name
  i_m_minimize_atom_index
  :::
  1 3 -1.593359 -1.026400 -2.195457 1 24 6 808080  C1  1
  2 3 -0.565628 -0.480762 -1.202775 1 2 6 A0A0A0  C2  2
  3 41 -1.560211 -0.493430 -3.146939 1 21 1 FFFFFF  H3  3
  4 41 -2.606114 -0.944213 -1.799475 1 21 1 FFFFFF  H4  4
  5 41 -1.413367 -2.081553 -2.404048 1 21 1 FFFFFF  H5  5
  6 41 -0.588336 -1.025736 -0.256676 1 21 1 FFFFFF  H6  6
  7 26 0.749607 -0.520029 -1.779849 1 43 7 5757FF  N7  7
  8 16 -0.772232 0.882337 -0.969039 1 70 8 FF2F2F  O8  8
  9 42 -1.525474 1.167314 -1.465735 1 21 1 FFFFFF  H9  9
  10 43 1.354087 0.054715 -1.209072 1 21 1 FFFFFF  H10  10
  11 43 1.121596 -1.457737 -1.735619 1 21 1 FFFFFF  H11  11
  :::
 } 
 m_bond[10] { 
  # First column is bond index #
  i_m_from
  i_m_to
  i_m_order
  :::
  1 1 2 1
  2 1 3 1
  3 1 4 1
  4 1 5 1
  5 2 6 1
  6 2 7 1
  7 2 8 1
  8 7 10 1
  9 7 11 1
  10 8 9 1
  :::
 } 
}

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

$SCHRODINGER/xtb opt-xtb_solv-0001.mae -optimize -solvation water -jobname=opt_xtb_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: 2025-4

Input structure: opt-xtb_solv-0001.mae
Output files

Note: With xTB, all frequency calculations are done numerically with finite-difference of gradients.

Example input file (opt_freq-xtb-0001.in):

&gen
xtb=1
igeopt=1
ifreq=1
&
&zmat
C1     -1.5933590000000  -1.0264000000000  -2.1954570000000
C2     -0.5656280000000  -0.4807620000000  -1.2027750000000
H3     -1.5602110000000  -0.4934300000000  -3.1469390000000
H4     -2.6061140000000  -0.9442130000000  -1.7994750000000
H5     -1.4133670000000  -2.0815530000000  -2.4040480000000
H6     -0.5883360000000  -1.0257360000000  -0.2566760000000
N7      0.7496070000000  -0.5200290000000  -1.7798490000000
O8     -0.7722320000000   0.8823370000000  -0.9690390000000
H9     -1.5254740000000   1.1673140000000  -1.4657350000000
H10     1.3540870000000   0.0547150000000  -1.2090720000000
H11     1.1215960000000  -1.4577370000000  -1.7356190000000
&

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

$SCHRODINGER/jaguar run -jobname=opt_freq_xtb_0001 opt_freq-xtb-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: opt_freq-xtb-0001.in
Output files