Desmond System Builder

The System Builder panel allows you to set up a biological system consisting of proteins, ligands, explicit solvent, membrane, and counter ions, so that you can perform simulations on the system with Desmond.

Backend implementation

Options

Column containing input

Select the column containing input structure

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

Use custom OPLS

Custom OPLS specified below will be used if this option is ON

Choose custom OPLS file

Select the custom OPLS file to be used

Settings...

On clicking "Settings" button, this node brings up the "Covalent Docking" Python panel for configuration.

Parameter flow variables

Any valid option for this node can be specified through flow variables. Only String variables are accepted.
Usage:
Flow variable prefix keyword: SystemBuilder
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 without a value, specify the option_name and the value as _off_ through the flow variable.

To remove an existing option with a value, specify the option_name and the value as _rm_ through the flow variable.

Views

Log of multisim

Log of multisim

Workflows

• MD simulation 1KNIME Hub
• MD simulation 1KNIME Hub
• MD simulation 1-2KNIME Hub
• MD simulation 1-2KNIME Hub
• MD simulation 1-3KNIME Hub
• Show all 6 workflows

Links

• No links available

Developers