Desmond System Builder

The System Builder node 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.

Platform Limitations: Linux only

Backend implementation

Options

Column containing input structures

Column in the input data table containing the input structures.

Output Column Structure

Choose the output columns:

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

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

Output only - Only Output structures

Location of output files

This is where the output CMS files will be stored.

Set Up Membrane...

Select this button to open the Membrane setup dialog.

Delete Membrane

If a membrane has been selected (through the Membrane Dialog), this button will be enabled and pressing will delete the current membrane options.

Solvent model: None

Do not use solvent. This allows running of simulations for a pure liquid,for example, or in a vacuum (low-density gas).

Solvent model: Predefined

Use one of the predefined solvent models, which you can select from this option menu. The available models are four water models, SPC, TIP3P, TIP4P, and TIP4PEW, and three organic solvents, DMSO, METHANOL, and OCTANOL.

Solvent model: Custom

Import a custom solvent system from file. Enter the solvent system file name in the text box, or click Browse, and navigate to the solvent system file in the file selector that is displayed.

Box shape

Select the box shape. Three basic shapes are provided: Cubic, Orthorhombic, and Triclinic. As special cases of the triclinic box shape, three other shapes are supported: Truncated octahedron, Rhombic dodecahedron xy-square, and Rhombic dodecahedron xy-hexagon.

Box size calculation method: Buffer

The simulation box size is calculated by using the given buffer distance between the solute structures and the simulation box boundary.

Box size calculation method: Absolute size

Specify the lengths of the sides of the simulation box size (and angles if necessary).

Distances or Size

Set the buffer distances or side lengths, in angstroms, in these text boxes. The label depends on the choice of boundary condition. The available text boxes depend on the box shape. For the Cubic, Truncated octahedron, Rhombic dodecahedron xy-square, and Rhombic dodecahedron xy-hexagon box shapes, only the text box for the a axis is available.

Angles

Specify the alpha, beta, and gamma angles for the box. This option is only active if you selected Triclinic box shape.

Excluded region

Define a region in which ions (both counter and salt) will not be placed. The region is defined in terms of a buffer zone around an atom selection. Enter the distance from the selected atoms that define the region from which ions will be excluded. Also enter an ASL expression to select atoms that will be used to define the exclusion region.

Ion placement: None

Do not add counter ions.

Ion placement: Neutralize

Neutralize the net charge of the system automatically by adding ions.

Ion placement: Add

Enter the number of ions to add in the text box and choose the ion type from the option menu.

Add salt

Select this option to add salt to the solution.

Salt concentration

Enter the salt concentration in mol dm-3. This value is used to calculate the number of ions in the system.

Salt positive ion

Choose a positive ion from these option menus to define the salt to be used to convert the pure solvent to a salt solution.

Salt negative ion

Choose a negative ion from these option menus to define the salt to be used to convert the pure solvent to a salt solution.

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Log of Desmond System Builder

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