QM Conformer & Tautomer Predictor — Options Pane

Set options for ring tautomers, charge and solvent.

To open this dialog box, click the Options link in the QM Conformer & Tautomer Predictor Panel.

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Options Pane Features

Include ring tautomers option

When generating ring tautomers, include tautomers that involve ring opening and ring formation.

Process rings recursively for max of N cycles option and text box

Run multiple cycles of ring tautomerization, using the output from each cycle as input to the next. Input rings can be opened in any cycle, and new rings formed. This procedure can generate polycyclic structures, possibly adding one ring per cycle to a ring system.

Size text boxes

Specify the minimum and maximum size of the rings that can be formed.

Charge adjustment tet box

Specify the number of protons (H+ ions) to be added to the structure before performing the search. A negative number means remove protons from the structure. This option is only available when tautomers are being generated. The program automatically detects the atoms in the molecule that are candidates for proton addition or removal (i.e. acidic or basic sites, sites that take part in tautomerization).

Solvent option menu

Specify the solvent in which the calculation should be run, from Water or None. The calculation in solvent is run using the PBF implicit solvation model.

Related Topics

Workflow Examples

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