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DelPhi v.4-The New Macromolecular Electrostatics Modeling (Manual release.01)

Summary: DelPhi v.4- The New Macromolecular Electrostatics Modeling
(Manual release.01)
DelPhi v.4 is the new version of the well-known and widely used DelPhi software package.
This manual describes the main features of the old program, as well as the new features. Whenever
possible, we have preserved compatibility with previous versions of DelPhi. People who are used to
older versions of DelPhi should not encounter any difficulties in this one. DelPhi v.4 is a software
package that calculates electrostatic potentials in and around macromolecules or geometrical
objects. It can solve the non-linear and linear forms of the Poisson Boltzmann equation using finite
difference methods on a GSZxGSZxGSZ cubical lattice. The user can specify the size of the ion
exclusion (or Stern) layer around the molecule and a variable probe radius to define the solvent
accessible surface. Different objects and molecules (or a combination of them) can be specified
using their own dielectric constant. Various boundary conditions such as periodic and focusing can
be used to model different systems like long periodic molecules or cell membranes. The output
from the program can be used to calculate molecular interactions, changes in pKa, solvation
energies and many other properties of interest.
The first versions have been written by Kim A. Sharp and Anthony Nicholls.
Surface algorithm was added by Sundaram Sridharan.
The new version is written by Walter Rocchia,


Source: Alexov, Emil - Department of Physics and Astronomy, Clemson University


Collections: Physics; Biology and Medicine