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 SDPBS" button.

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Solver  ? Select a PBE solver.

Mesh Parameters

Domain shape  ? Select the geometric shape of the computational domain Ω
Cubic: Generate a cubic shape domain
Spherical: Generate a spherical shape domain
Default: Cubic
Note: Only used for finite element solver
Surface type  ? Select type of interface surface Γ
Gaussian surface: Use GAMer Gaussian surface and marching-cube method
SES: Use GAMer solvent-excluded surface
SAS: Use EDT solvent-accessible surface
Default: Gaussian surface
This job may take a few minutes. When the job is complete, a free energy value, download link, visualization, and output log will be updated on this page.
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

3Dmol instructions here.

Controls

Data range for surface map color scale  ? Set the cut-off values used to determine the color of each vertex on the current surface. Tweak these values to achieve a preferred color contrast in the color mapping.
Set: Set the above min and max values as the color-value map range.
Autoscale: Reset the color-value map range to the default range between the data's absolute min and max.

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 electrostatic potential file in .dx format for visualization in JSmol.
    7. 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.