Input Files

The input files of EGO for a molecular dynamics simulation consist of atom coordinates, connectivity, energy parameter and a definition file for the so-called structural units. The atom coordinate and residue information is taken from Brookhaven Protein Data Bank (PDB) format files. The atom type, mass, partial charge, and connectivity information (bonds, angles, etc.) is taken from X-PLOR PSF files. The energy parameters defining force constants and equilibrium coordinates are taken from X-PLOR parameter (paramxxx.xxx) files. Furthermore, the structure adapted multipole method on which FAMUSAMM is based and which is responsible for the approximate but fast calculation of Coulomb forces, needs the definition of so-called structural units. These structural units are defined in the input file units.def.