Calculate Electrostatic Solvation Energy

Upload File, Adjust Parameters and Submit Job

Before submitting a job, prepare a PQR file of the biomolecule you wish to analyze. This can be done by first downloading a PDB file of the biomolecule from the RCSB Protein Data Bank, and then converting it to a PQR file by using PDB2PQR. A sample PQR file for the protein with PDB ID "4PTI" can be downloaded here.

After preparing the PQR file:

  1. Upload the PQR file.
  2. Adjust basic parameters, or use default parameter values.
  3. (Optional) Adjust additional parameters (located in tabs).
  4. Submit the job by clicking the "Run SMPBS" button.
Solver  ? Select a SMPBE solver.

Mesh Parameters

Iterative Solver Parameters

Linear solver type  ? Select the linear iterative solver type.
Default: Generalized Minimum Residual
This job may take a few minutes. When the job is complete, the Visualization & Results tab and Output Log tab will be updated.
Reload the page to run a new job.

View Visualization, Free Energy Value, and Download Results

After submitting the job, please wait patiently for your results.

When your results are successfully retrieved from the server, you should see the following changes on the page:

  • The "Visualization" section below should automatically display the uploaded biomolecule, and electrostatic potential results can be manually mapped onto a generated surface.
  • The "Electrostatic Solvation Free Energy" section below should show the solvation energy value.
  • The "Download" section below should show a link to download a zipped file containing various result files.
  • The "Output Log" section in the next tab should show a text log of the computation performed by our software package.


Visualization of biomolecules and surfaces is performed by 3Dmol.js, a modern Javascript library for visualizing 3D molecular data.

Model Canvas

A simple biomolecule, 2LZX, is drawn by default. Left-click and drag the mouse inside the canvas to rotate the molecule. Left-click an atom to display its label.

Controls - Molecule Tab

In this tab, you can change the molecule being displayed, change the style of the atoms of the molecule, and recenter the view of the molecule.

Controls - SMPBS Surface

In this tab, you can load a custom surface and map electrostatic results onto that surface, using files or data that you download from our server after a successful job submission. You can also adjust the properties of the surface and color map.

An OFF file contains the data for creating a molecular surface. A DAT file contains the data for mapping electrostatic values as colors onto that surface. Both types of files are included in the ZIP folder you can download below after your job completes.

For best results, the OFF and DAT file should correspond to the molecule you have loaded into the viewer, and you should load the OFF file first, followed by the DAT file.

Immediately following a job submission, the OFF and DAT data will also be saved to memory. Since changing the molecule or generating a surface will remove any existing surfaces, this is useful when you want to re-load the custom surface and color map without navigating through the file system to locate the appropriate files.

Controls - 3DMol Surface

In this tab, you can tell 3Dmol.js to generate a molecular surface using its own algorithms. You can also show atomic partial charge as a color mapping (if the data is available), and adjust properties of the surface.


Event log

    Electrostatic Solvation Free Energy

    Submit a job to view the free energy value.

    Download Files

    Click Download to get the following files in zipped form:

    1. The protein data in .pqr format.
    2. The mesh file in .off format.
    3. The mesh file in .xml format (for use with DOLFIN).
    4. Two electrostatic potential files in .pvd format for visualization via Paraview (Not saved by default, adjust output parameter settings to save these files)
    5. The electrostatic potential file in .dat format for PBE solution u and its components G, Psi, and Phit.
    6. The parameter file, Parameters.ini, that was used as input for this calculation.
    Submit a job to download your results.

    View Output Log

    After submitting the job, please wait patiently for your results.

    When your results are successfully retrieved from the server, the "Output Log" section should display a text log of the computation performed by our software package.

    Output Log

    Submit a job to view the output log.