Calculate Electrostatic Solvation Energy

Upload Files

Before submitting a job for computing an electrostatic solvation free energy, you upload biomolecular data files in the following steps:

  1. Enter the PDB ID of a VDAC.
  2. Upload the PQR file if you have one. Otherwise, the server generates one for you by using PDB2PQR.
  3. Upload the PDB file if you have one. Otherwise, the server downloads one from the OPM Database.
  4. Upload the XML mesh file if you have one. This can speed up the calculation. Otherwise, the server generates one for you. In this case, you can adjust mesh parameters by clicking the tab Mesh.

Adjust Parameters

You can adjust the model, mesh, solver, and output parameters located in the tabs Basic, Mesh, Solvers, and Output, respectively. Or simply use the default parameter values. We define a box domain, \(\Omega\), by \[ \Omega = [px_{\text{min}} - \Delta x_1, px_{\text{max}} + \Delta x_2] \times [py_{\text{min}} - \Delta y_1, py_{\text{max}} + \Delta y_2] \times [pz_{\text{min}} - \Delta z_1, pz_{\text{max}} + \Delta z_2] \] where \([px_{\text{min}}, px_{\text{max}}] \times [py_{\text{min}}, py_{\text{max}}] \times [pz_{\text{min}}, pz_{\text{max}}]\) is the smallest box containing the ion channel protein, which is determined by the server. You can adjust the box size by entering the parameters \(\Delta x_1\), \(\Delta x_2\), \(\Delta y_1\), \(\Delta y_2\), \(\Delta z_1\), and \(\Delta z_2\) in the tab Mesh.

Model Parameters

SMPBIC Model ? Select which model to use.
uSMPBIC: Solve the uniform SMPBEic model.
nuSMPBIC: Solve the non-uniform SMPBEic model.
PBIC: Solve the PBEic model.
Default: uSMPBIC.
Reference State for Free Energy ? Select reference environment for computing solvation free energy.
Default: Water environment.
Initial Iteration for solving nuSMPBIC  ? Select a model for the initial iteration for solving the nonuniform SMPBIC model.
Linear uSMPBIC: Perform calculations using the linear uniform SMPBIC model.
Non-Linear uSMPBIC: Perform calculations using the non-linear uniform SMPBIC model.
Default: Linear uSMPBIC.
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

Linear Solver Type computing ? Select the linear solver type.
Default: LU Decomposition
Linear Solver Type for \(\tilde{\Phi}\) ? Select the linear solver type for computing \(\tilde{\Phi}\).
Default: Generalized Minimum Residual
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.
Use non-zero initial guess? ? Select whether to use a non-zero initial guess for linear iterative solver.
Yes: Use a non-zero initial guess
No: Use zero as initial guess
Default: Yes
Print convergence information? ? Select whether to output the iterative information of linear iterative solver.
Yes: Output iterative information
No: No output
Default: No
Submit the job by clicking the "Run SMPBICS" button. 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.
You must reload the page to run a new job.

Visualization, Free Energy, 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 should automatically display a molecular structure of the uploaded VDAC, and a color mapping of the computed electrostatic potential values onto the generated molecular surface of the VDAC.
  • The "Electrostatic Solvation Free Energy" section should show the electrostatic solvation free energy value.
  • The "Download Files" section should show a link to download a zipped file containing result files.
  • The "Output Log" section in the next tab should show a text log of the computation performed by our software package. It starts with the mesh generation information such as mesh data and computer performation data. It then gives the SMPBICS performation data, the solvation free energies, and the parameter values used in the calculation.

Visualization

A VDAC biomolecule, 3EMN, 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 molecular surface and map electrostatic values 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 electrostatic values defined on that surface. Both files are included in the ZIP folder you can download below after your job completes.

For best results, 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 - Paraview Glance

In this tab, you can use ParaView Glance to visualize the finite element meshes of the simulation box domain Ω, the protein domain Dp, the solvent domain Ds, and the membrane domain Dm. You also can use Paraview Glance to visualize the electrostatic potential functions and ionic concentration functions in color-mappings onto these meshes. To do so, you click the tab to open Glance. You then load a vtu file into Glance by hitting the “Open” button on the top-right toolbar.

Paraview Glance is an open-source web application developed at Kitware that can be used to visualize many data types. Its usage documentation can be found in the website https://kitware.github.io/glance/doc/.

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 parameter file, Parameters.ini, that was used as input for this calculation.
    2. The protein data bank (PDB) file in .pdb format.
    3. The protein data file in .pqr format
    4. The mesh file in .xml format (for use with DOLFIN).
    5. The molecular surface mesh file in .off format.
    6. The electrostatic potential file in .dat format for the electrostatic potential u and its components G, Psi, and Phit.
    7. Electrostatic potential and ionic concentration files in .pvd and .vtu formats for visualization via Paraview (Adjust output parameter settings to not save these files)
    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.