stko.MacroModelMD

class stko.MacroModelMD(macromodel_path, output_dir=None, timeout=None, force_field=16, temperature=750, conformers=50, time_step=1, eq_time=10, simulation_time=200, maximum_iterations=2500, minimum_gradient=0.05, restricted_bonds=None, restricted_bond_angles=None, restricted_torsional_angles=None)[source]

Bases: MacroModel

Runs a molecular dynamics conformer search using MacroModel.

Parameters:

macromodel_path (str) – The full path of the Schrodinger suite within the user’s machine. For example, on a Linux machine this may be something like '/opt/schrodinger2017-2'.
output_dir (str | None) – The name of the directory into which files generated during the optimization are written, if None then uuid.uuid4() is used.
timeout (float | None) – The amount in seconds the MD is allowed to run before being terminated. None means there is no timeout.
force_field (int) – The number of the force field to be used.
temperature (float) – The temperature in Kelvin at which the MD is run. Cannot be more than 99999.99.
conformers (int) – The number of conformers sampled and optimized from the MD. Cannot be more than 9999.
simulation_time (float) – The simulation time in ps of the MD. Cannot be more than 999999.99.
time_step (float) – The time step in fs for the MD. Cannot be more than 99999.99.
eq_time (float) – The equilibration time in ps before the MD is run. Cannot be more than 999999.99.
maximum_iterations (int) – The maximum number of iterations done during the optimization. Cannot be more than 999999.
minimum_gradient (float) – The gradient at which optimization is stopped. Cannot be less than 0.0001.
restricted_bonds (set | None) –
A set of the form
```
restricted_bonds = {
    frozenset((0, 10)),
    frozenset((3, 14)),
    frozenset((5, 6))
}
```
Where each frozenset defines which bonds should have a fixed length via the atom ids of atoms in the bond.
restricted_bond_angles (set | None) –
A set of the form
```
restricted_bonds = {
    frozenset((0, 10, 12)),
    frozenset((3, 14, 7)),
    frozenset((5, 8, 2))
}
```
Where each frozenset defines which bond angles should have a fixed size via the atom ids of atoms in the bond angle.
restricted_torsional_angles (set | None) –
A set of the form
```
restricted_bonds = {
    frozenset((0, 10, 12, 3)),
    frozenset((3, 14, 7, 4)),
    frozenset((5, 8, 2, 9))
}
```
Where each frozenset defines which torsional angles should have a fixed size via the atom ids of atoms in the torsional angle.

Examples

Molecular dynamics can be run on any stk.Molecule using this class. Restrictions can be applied, but are not by default. This class collects a series of conformers from the trajectory, optimises them, then returns the lowest energy conformer.

import stk
import stko

mol = stk.BuildingBlock('NCCCN')
optimizer = stko.MacroModelMD(
    macromodel_path='/path/to/macromodel/',
    conformers=40,
)
mol = optimizer.optimize(mol)

Methods

optimize

Optimize mol.

optimize(mol)[source]

Optimize mol.

Parameters:: mol (MoleculeT) – The molecule to be optimized.
Returns:: The optimized molecule.
Return type:: MoleculeT