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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