DelPhi

DelPhi takes as input a coordinate file format of a molecule or equivalent data for geometrical objects and/or charge distributions and calculates the electrostatic potential in and around the system, using a finite difference solution to the Poisson-Boltzmann equation. DelPhi is a versatile electrostatics simulation program that can be used to investigate electrostatic fields in a variety of molecular systems. The current version is fast and accurate.

New features of DelPhi include solutions to the nonlinear form of Poisson-Boltzmann equation which provide more accurate solutions for highly charged systems; solutions to mixtures of salts of different valence; solutions to different dielectric constants to different regions of space; higher precision in the finite difference scheme through the derivation of the expression for electrostatic free energy; and estimation of the best relaxation parameter at run time. All of these features enhances the speed and versatility of DelPhi to handle more complicated systems and finite difference lattices of extremely high dimension.

Download software

Click here to download DelPhi.

System requirements

Unix version runs on SGI IRIX operating systems. Fortran 77 and C compilers are required. Executable is also provided in tar file.

Linux version requires Fortran and C compilers. Executable is also provided in tar file.

PC version requires Fortran and C compilers. Executable is also provided.

AIX IBM version requires xlf and xlC compilers. Executable for AIX 5.1 is also provided.

Mac version runs on Macintosh. Executable is also provided.The PowerPC Mac executable version of delphi is dynamically linked to IBM XL compiler libraries. It will not run unless you have these libraries on your local system.

Intel Mac version runs on Macintosh with Intel processor. Executable is also provided.

Documentation

Click on the links below to learn more about using DelPhi.

• How to run DelPhi

• New DelPhi functions

• Statements and Functions

• Index of Statements and their shorthands

• Sample parameter file

• Glossary

• Notes on input parameters

• Standard file formats

• New GRASP compatible phimap format

• How To Make an Electrostatic Surface with Delphi and PyMol

• Sample input file for generating GRASP2 and PyMOL Electrostatic Surface

Click here to download user manual as pdf.

Examples and sample data

Click here to download examples.

Click here to download sample data.

References

Rocchia W, Alexov E, Honig B. Extending the applicability of the nonlinear Poisson-Boltzmann equation: multiple dielectric constants and multivalent ions. J Phys Chem B. 2001;105(28):6507–14.

Honig B, Nicholls A. Classical electrostatics in biology and chemistry. Science. 1995 May 26;268(5214):1144-9.

Yang AS, Gunner MR, Sampogna R, Sharp K, Honig B. On the calculation of pKas in proteins. Proteins. 1993 Mar;15(3):252-65.

Nicholls A, Honig B. A rapid finite difference algorithm, utilizing successive over-relaxation to solve the Poisson-Boltzmann equation. J Comp Chem. 1991;12:435-45.

Gilson MK, Honig B. Calculation of the total electrostatic energy of a macromolecular system: solvation energies, binding energies and conformational analysis. Proteins. 1988;4(1):7-18.

Gilson MK, Sharp K, Honig B. Calculating the electrostatic potential of molecules in solution: method and error assessment. J Comp Chem. 1987;9:327-35.

Klapper I, Hagstrom R, Fine R, Sharp K, Honig B. Focussing of electric fields in the active site of Cu-Zn superoxide dismutase: effects of ionic strength and amino acid modification. Proteins. 1986 Sep;1(1):47-59.

Acknowledgments

DelPhi is supported by a funding from the NIH Grant # GM030518.

Contact

Please address all DelPhi related questions to ealexov@clemson.edu, switham@clemson.edu, subhras@clemson.edu.