Calculate Binding Energy

Upload Files, Adjust Parameters and Submit Job

Before submitting a job, prepare three PQR files for the biomolecule complex and its two components (component A and component B). This can be done by first downloading PDB files of the biomolecules from the RCSB Protein Data Bank, and then converting them to PQR files by using PDB2PQR. After preparing the PQR files:

  1. Upload the PQR files for the complex, component A, and component B separately.
  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 for Protein Complex

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

Mesh Parameters for Protein Component A

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

Mesh Parameters for Protein Component B

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 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 Binding Free Energy" section below should show a table summarizing the computation results.

Electrostatic Binding Free Energy

Submit a job to view the free energy values.