Simulation Setup

System that contains target, probes, water, and counter ions for druggability simulations can be prepared using the following interface:


Input Files

.psf and .pdb files for the target protein are required from the user. You can learn how to prepare these files from NAMD tutorials.

Options & Parameters

  1. First, select .psf (structure) and .pdb (coordinate) files. You can use the MDM2 files provided for this tutorial. Alternatively, structure and coordinate files for a protein of interest can also be used. These files should contain all atoms required for protein stability and function, these may include cofactors and metal atoms. Crystallographic water molecules may also be retained in the

  2. Select a probe composition that will complement the surface properties of the target protein. Note that, probe percentages must sum up to 100. Acetate and isopropylamine percentages will be equal to each other so that opposite probe charges are balanced.


    It is possible to set all probe percentages to zero. The final system will not contain any probes. This may be used as a control simulation, to see how the target protein behaves in the absence of probes.

  3. Enter simulation box padding (distance from the protein to box surfaces) and select whether you would like to add counter ions. Druggability GUI uses Solvate and Autoionize plugins to add water, probes, and ions.

  4. Select output folder, file prefix, and number of simulations that you want to perform. Performing multiple simulations to see whether results are reproducible is always a good idea.

Output Files

Output will be prefix.psf and prefix.pdb files of the system that contain target protein, water, ions, and probe molecules (if selected). You system should look like the following:


In addition, you will see prefix_min, prefix_sim, parameters folders that contain input for molecular dynamics simulations.

For a summary of contents of the final system, see prefix.log file.


Now you need to run druggability simulations. See file for NAMD commands that you need to execute. When simulations are complete, you can continue with following analysis steps.