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APBS

Calculates polar solvation energy from user supplied structures using the Adaptive Poisson-Boltzman Solver (APBS) software package.

Accessibility

The APBS module is accessible from the Analyze section of the main menu.

Basic Usage

The purpose of the module is calculate the polar solvation energy for input structures. If the input structures are specified as a multi-frame DCD or PDB file, the polar solvation energy is calculated for each frame in the file. The module incorporates the APBS software package and writes the APBS input file for simplified execution of the calculation.

Notes

• Detailed information of how solvation energies are calculated with APBS, including a description of APBS input file parameters, can be found here.
• The included PDB2PQR package is used to modify a PDB file, replacing the occupancy column with the atomic charge and the temperature factor column with the radius.
• pKa values are predicted by the included PROPKA package.

Screen Shots and Description of Input Fields

This example calculates solvation free energies for a 10-mer polypeptide molecule.

• run name user defined name of folder that will contain the results.

• reference pdb PDB file with naming information and coordinates of the starting structure.

• input filename (dcd or pdb): DCD or PDB file with coordinates that will be used to calculate polar solvation energies.

• pH Desired pH value.

• temperature (K) Desired temperature.

• ion concentration (M) Molar concentration of solute ion.

• ion charge Charge of ion.

• largest ion radius Radius of ion.

Example Output

Results are written to a new directory within the given "run name" as noted in the output.

Several files are generated and saved to the "run name"/apbs directory.

run_0/apbs/ten_mer.pdb                  -- the reference PDB file
run_0/apbs/apbs_00001.pdb               -- the input PDB file 
run_0/apbs/abps_00001_pdb2pqr.dat       -- the PDB2PQR output file
run_0/apbs/apbs_00001.propka            -- the pKa predictor output file
run_0/apbs/apbs_00001.pqr               -- the PDB file with atomic charge and radius
run_0/apbs/apbs_00001.in                -- input file for APBS
run_0/apbs/apbs_00001_io.mc             -- I/O capture from APBS (for debugging)
run_0/apbs/apbs_00001.out               -- output file containing the solvation energy

The polar solvation energy is found at the bottom of the file ending in .out. In this example, it is 557.4 kJ/mol. If there is more than one frame in the input PDB or DCD file, there will be multiple .out files.

Visualization

None

Files Used and Created in Example

• input files

  ten_mer.pdb

• output files

  ten_mer.pdb

  apbs_00001.pdb

  apbs_00001_pdb2pqr.dat

  apbs_00001.propka

  apbs_00001.pqr

  apbs_00001.in

  apbs_00001_io.mc

  apbs_00001.out

Limitations

Currently, users cannot submit their own APBS input files to access other functionality of the APBS-PDB2PQR package.

Reference(s) and Citations

1. PDB2PQR: an automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations T. J. Dolinsky, J. E. Nielsen, J. A. McCammon, N. A. Baker, Nucleic Acids Res, 32, W665-W667, (2004). BIBTeX, EndNote, Plain Text
2. PDB2PQR: Expanding and upgrading automated preparation of biomolecular structures for molecular simulations T. J. Dolinsky, P. Czodrowski, H. Li, J. E. Nielsen, J. H. Jensen, G. Klebe, N. A. Baker, Nucleic Acids Res, 35, W522-W525, (2007). BIBTeX, EndNote, Plain Text
   
3. Electrostatics of nanosystems: application to microtubules and the ribosome N. A. Baker, D. Sept, S. Joseph, M. J. Holst, J. A. McCammon, Proc. Natl. Acad. Sci. USA 98, 10037-10041 (2001). BIBTeX, EndNote, Plain Text
4. Small-Angle Neutron Scattering Study of a Monoclonal Antibody Using Free-Energy Constraints N.J. Clark, H. Zhang, S. Krueger, H.J. Lee, R.R. Ketchem, B. Kerwin, S.R. Kanapuram, M.J. treuheit, A. McAuley, J.E. Curtis, J. Phys. Chem. B, 117, 14029-14038 (2013). BIBTeX, EndNote, Plain Text

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