DelPhiController

DelPhiController is an interface to DelPhi, which uses the finite-difference Poisson-Boltzmann equation to calculate electrostatic potentials in and around molecules. DelPhi is not included with Chimera; DelPhiController works with the academic version available from the Honig Lab or the DelPhi development team. For more details, see the DelPhi documentation at either of those sites. See also: APBS, Coulombic Surface Coloring

There are several ways to start DelPhiController, a tool in the Surface/Binding Analysis and Volume Data categories (including from the Volume Viewer Tools menu). It has three sections organized like index cards: Input, Parameter, and Output. Clicking a tab brings the corresponding card to the front.

Clicking Run initiates the DelPhi calculation; the time required depends on the system and parameters, but generally ranges from nearly instantaneous to minutes. Cancel dismisses the DelPhiController panel, while Help opens this manual page in a browser window.

The Electrostatic Surface Coloring tool for coloring molecular surfaces by potential will appear after the potential map (*.phi file) has been created. Alternatively, the map can be shown as isopotential surfaces; these are not displayed automatically, but can be shown by starting Volume Viewer and clicking the eye icon or by using the volume command.

At a minimum, the required inputs are a structure of interest, a radius file, a charge file, and the location of the DelPhi executable. Any adjustments in Parameter settings and Output file names and locations must be made before the calculation is started.

The structure can be a model already open in Chimera or the contents of a local PDB file, specified using the pulldown menu in the Molecule section of the dialog.

• if Chimera Model, use Browse... to specify a model that has already been opened in Chimera
• if PDB File, use Browse... to specify the file or enter a pathname manually

The locations of other input files can be entered manually or filled in with Browse. When DelPhi has been run successfully with DelPhiController, the input file locations are saved in a user's preferences file.

• DelPhi Executable (required) - name and location of the DelPhi executable. If a pathname is not already stored in the preferences file, this will be filled in automatically provided the executable is on the user's path (and, on a Mac, provided Chimera is started from the terminal command line).
• Atomic Radii File (*.siz, required) - a radius assignment file; see the DelPhi development site for examples
• Atomic Charge File (*.crg, required) - a charge assignment file; see the DelPhi development site for examples
• Potential File (for focussing) (*.phi) - a previously calculated electrostatic potential map, not required unless focussing is being performed
• PDB Input for Site Potentials (*.pdb) - a PDB file, not required unless an output site potentials file is specified; however, if such an output is specified and this field is left blank, the coordinates of the structure for which the potential is being calculated will be used

• add or edit specifications in the assignment files so they will match atom/residue names in the structure
• edit atom/residue names in the structure so they will match specifications in the assignment files

DelPhi uses many parameters, and although reasonable defaults are supplied, what values are optimal will depend on the situation. Note that the defaults in DelPhiController may differ from those described in the DelPhi documentation.

Basic:

• Automatic Convergence (on by default) - automatically calculate the number of iterations needed to attain convergence
• Calculate GRASP Surface (off by default) - generate a GRASP-format surface file named grasp.srf in the same location as the output electrostatic potential map
• Box Fill (%) (60 by default) - percentage of the grid that the largest dimension (X, Y, or Z) of the structure will fill. Smaller percentages will increase the accuracy of the boundary conditions, but yield a coarser representation of the molecule. For a single run (i.e., when focussing is not done), reasonable compromise values are ~60% for viewing potentials outside a protein, ~90% for solvation energy calculations.
• Grid Scale (1.2 by default) - grid resolution, points per Å
• Probe Radius (1.4 by default) - radius (Å) of the solvent probe used to define the solvent-excluded surface; values of 1.4-1.8 Å are reasonable for water

• Fancy Charge Distribution (off by default) - distribute charges to grid points using a spherical distribution (otherwise linear cubical interpolation will be used)
• Log File Convergence (off by default) - write convergence information to the output log file
• Log File Potentials (off by default) - write potentials to the output log file
• Periodic Boundary (X) (off by default)
• Periodic Boundary (Y) (off by default)
• Periodic Boundary (Z) (off by default)
• Boundary Conditions - how to set boundary potentials where periodicity is not used
  • Zero
  • Debye-Huckel Dipole
  • Focussing - use a potential map from a previous run to set the boundary conditions for the current run (requires an input electrostatic potential map)
  • Debye-Huckel Total (default) - Coulombic; recommended unless focussing is being performed
• Interior Dielectric Constant (2 by default) - dielectric constant inside the molecule; 2 represents electronic polarizability
• Exterior Dielectric Constant (80 by default) - dielectric constant outside the molecule; 80 approximates water
• Grid Convergence (0.0 by default)
• Ionic Strength (0.0 by default) - ionic strength (M) of the solvent; physiological ionic strength is approximately 0.145 M
• Ion Radius (0.0 by default) - thickness (Å) of the ion exclusion layer, relevant when ionic strength > 0.0; a value of 2.0 Å is reasonable for sodium chloride
• Non-Linear Iterations (0 by default)

The results of any requested Energy calculations will be written to the log file.

• Total Grid - charge multiplied by potential, summed over all charges within the grid; contains the real electrostatic energy plus the grid self-energy
• Reaction Field - interaction of all charges with the induced surface charge within the grid; solvation energy is generally obtained by taking the difference in this value between calculations using different exterior dielectric constants
• Coulombic - energy calculated with Coulomb's law to bring all charges from infinity to their locations in the interior dielectric medium

• Potential File (phimap) (*.phi) - DelPhi electrostatic potential map; potentials are in kT/e (0.593 kcal/mol at 25°C)
• Site Potentials File (*.frc) - file containing the potentials and fields at coordinates from an input file "for site potentials"
• Dielectric Map File (*.eps) - binary dielectric bit map
• Modified PDB File (*.pdb) - coordinates of the input structure in PDB format, except with the assigned radius and charge of each atom placed in columns 55-60 (replacing occupancy) and 61-67
• Log File (*.log) - always produced; reports control parameter settings, calculation times, and other information