SODIUM places the required number of sodium ions around a (simulated) system of electric charges, e.g., the atoms of a biological macromolecule (protein, DNA, protein/DNA complex). The ions are placed in the nodes of a cubic grid in which the electrostatic energy achieves the smallest values. The energy is re-computed after placement of each ion. A simple Coulombic formula is used for the energy. The coordinates of the placed ions are printed out in the PDB format for further usage. Trivial modifications to the program should allow the placement of any combination of multivalent ions of different charges.
|Tags||Scientific/Engineering Bioinformatics Chemistry Medical Science|
|Operating Systems||OS Independent|
Release Notes: This release adds speed improvements, bugfixes, and improvements to the documentation.