Calculate Electrostatic Solvation Energy

1. 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 either of the "Run SDPBS" buttons.
Solver  ? Select a PBE solver.

Mesh Parameters

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.

2. View 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 "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 "Visualization" section below should automatically display the uploaded biomolecule, and electrostatic potential results can be manually mapped onto a generated surface.
  • The "Output Log" section at the bottom of the page should show a text log of the computation performed by our software package.

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.

Visualization

Visualization of biomolecules and surfaces is performed by JSmol, an open source framework and HTML5 applet for viewing 3D chemical structures. Most functionalities of JSmol are available via a context menu, accessible by right-clicking inside the JSmol window. We have replicated the more relevant functions in the adjacent control section for ease of use.

Before running a job

A simple biomolecule, 2LZX, is drawn by default. The surface electrostatic potential mapping of 2LZX has been pre-computed, and can be viewed by manually mapping it onto a generated surface. See the directions for "Mapping electrostatic potential to surface" below.

After running a job

Your uploaded biomolecule will be drawn automatically, but the computed electrostatic potential results will not yet be mapped onto the molecule. See directions below.

Mapping electrostatic potential to surface

To view computed electrostatic potential results as a colored map on the biomolecule surface:

  1. Display a Jmol-generated surface by clicking "Show filled surface" under "Surface display options."
  2. (Optional) Set the generated surface type, color gradient, and surface translucency.
  3. Map the computed results onto the surface by clicking "Yes" under "Map electrostatic potential results to surface."
Our current surface visualization method maps interpolated results onto a surface generated by JSmol. This method does not reflect the accuracy of our computed results, and we are currently exploring better options. In the downloaded zip folder, the interpolated results are found in the .dx file, while the actual surface potential results are found in the .dat file under column "Phi," corresponding to rows where the "Domain" column value is 3.

Controls

Output Log