What it does
Packmol creates initial MD configurations from input molecules - for example, creating a water and urea mixture.
How it works
- Select a molecule file type e.g. pdb, xyz
- Select a single molecule from your history (can select multiple)
- For each molecule:
- choose how many molecules to create (number variable)
- optionally choose:
- molecular radius
- how to number the molecules (resnumber variable)
- choose one or more placement constraint(s). Each constraint has different parameters:
- for example, specify placement inside a cube of size 40 Angstroms placed at the origin
- all units are in Angstroms for distances and degrees for angles
Outputs created
- A pdb file; view this in Galaxy by clicking on the 'visualize' icon and choosing a viewer. The NGLViewer works well for small molecules.
- A packmol input script (for debugging and repeatability)
User guide and documentation
Known issues
- fixed constraint only allows 1 atom but this is not set for the user. The user has to set this parameter. The job may fail.