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Prime Energy

Schrödinger extension for KNIME Workbench version by Schrödinger

Evaluate the energy and its components for one or more proteins

Backend implementation

scripts/refinestructCLI.py run by cmdRunner.py
The script refinestructCLI.py is passed to cmdRunner.py to implement this node.


Column containing input structures
Select column in the input data table containing the structures
Output Column Structure
Choose the output columns:

Input plus Output - The input columns are included in the output.

Output replaced within Input columns - The output columns are the same as the input, with the output structures replacing the input column selected

Output only - Only Output structures

Solvation model
Choose a continuum solvation model for the refinement. The choices are:

VSGB - Use the variable-dielectric generalized Born model, which incorporates residue-dependent effects. The solvent is water.

Vacuum - Do not include solvation.

Chloroform - Use chloroform as the solvent, modeled with the Surface Generalized Born (SGB) method.

Force Field
Choose the force field to use for the refinement. The default is OPLS2005.
Use Crystal Symmetry
If crystal symmetry is known for this protein, apply periodic boundary conditions so that the crystal symmetry is satisfied. The protein is refined in the presence of its crystallographic neighbours
Set the dielectric constant for the (continuum) solvent.
Include Log in output
Include the Prime log file as a column in the output data table
Parameter flow variables
Any valid option for this node can be specified through flow variables. Only String variables are accepted.
Flow variable prefix keyword: PrimeEnergy
Note: To specify an option as flow variable, the flow variable name should be like:
keyword-option_name for single-dash option
keyword--option_name for double-dash option

To add a new option with value, specify the option_name and the corresponding value through flow variable.

To add a new option without value, specify the option_name and the value as _on_ through flow variable.

To override an existing option's value in the command line, just specify the option_name and the new value through the flow variable.

To remove an existing option from command line, just specify the option_name and the value as _off_ through the flow variable.

To pick the value from a column in the input table, specify the option_name and the value as :column_name: through the flow variable. Any column other than String, Integer and Double types will be written to a file and the file name is added as the option value.

Input Ports

Molecules in Maestro format

Output Ports

Molecules in Maestro format with calculated energies

Best Friends (Incoming)

Best Friends (Outgoing)



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