Calculates polar solvation energy from user supplied structures using the Adaptive Poisson-Boltzman Solver (APBS) software package.
The APBS module is accessible from the Analyze section of the main menu.
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.
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.
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.
Currently, users cannot submit their own APBS input files to access other functionality of the APBS-PDB2PQR package.
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