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 one of the three following options:

  1. Upload a PQR file of the biomolecule.
  2. Upload a PDB file of the biomolecule. The SMPBS server will generate a PQR file using the PDB2PQR software package.
  3. Input a 4-character PDB ID for the biomolecule. The SMPBS server will use it to download a PDB file from the RCSB Protein Data Bank and then generate the PQR file using the PDB2PQR software package.

A sample PQR file for the protein with PDB ID "4PTI" can be downloaded here: (4PTI)

After preparing the PQR file:

  1. Adjust basic parameters, or use default parameter values.
  2. (Optional) Adjust additional parameters (located in tabs).
  3. Submit the job by clicking the "Run SMPBS" button.

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Upload a biomolecule  ? Select one of the following three options to upload a biomolecule.
PQR File: Upload a PQR file.
PDB File: Upload a PDB file to be converted to a PQR file by PDB2PQR.
PDB ID: Enter a 4-character PDB ID to let the web server generate a PQR file.
Default: PQR File.

Basic Parameters

Model ? Select which model to use for computing solvation free energies.
uSMPBE: The uniform SMPBE model.
nuSMPBIC: The non-uniform SMPBE model.
PBE: The PBE model.
Default: uSMPBIC.

Mesh Parameters

Forcefield options for PDB2PQR ? Select which forcefield option to use.
Default: CHARMM.
Note: Only used when no PQR file is provided.
Note: --drop-water and --include-header enabled by default.
Output naming scheme for PDB2PQR ? Select which output naming scheme to use.
Default: CHARMM.
Note: Only used when no PQR file is provided.

Iterative Solver Parameters

Dirichlet boundary condition  ? Select the Dirichlet boundary condition of the SMPBE solution on the boundary of the computational domain.
Zero: Use zero boundary value condition
MDH: Use multiple Debye-Huckel boundary value condition
Default: Zero
Finite element degree  ? Select the finite element degree.
Type: Integer
Range: 1-2
Default: 1
Linear solver type  ? Select the linear iterative solver type.
Default: LU Decomposition
Preconditioner  ? Select the preconditioning method for solving PBE linear systems.
Default: Incomplete LU decomposition
Note: Not valid if the LU decomposition linear solver is used.
Print convergence information?  ? Select whether to output the iterative information of linear iterative solver.
Yes: Output iterative information
No: No output
Default: No
Initial guess option  ? Select initial guess for solving system of nonlinear equations.
Zero: Use zero as initial guess
Linear PBE: Use linear PBE solution as initial guess
Default: Linear PBE
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

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

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

Visualization

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 load a molecule file, download a PDB file, 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.

Controls - Paraview Glance

In this tab, you can use Paraview Glance to view the meshes of the protein and solvent regions and the color mapping of computed electrostatic and ionic concentration values onto the meshes.

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 .pdb and .pqr formats.
    2. The mesh ɸ file in .off format.
    3. The mesh box file in .xml format (for use with DOLFIN).
    4. Two electrostatic potential files in .pvd format for visualization via Paraview Glance
    5. The electrostatic potential file in .dat format for SMPBE 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.