II. Initial Coordinates

The psf only specifies what atoms are involved, how they're connected, and what interactions determine the system's energy. Next, we need to place the atoms somewhere. Simulations are generally begun with experimentally determined coordinates, typically from the Brookhaven Protein Data Bank. Structures determined by X-ray diffraction lack positions for hydrogen atoms, while those determined by neutron diffraction (less common) or nuclear magnetic resonance do not. For X-ray structures, the hydrogen positions can be assigned by CHARMM (using the HBUIld command). Initial coordinates of small systems can also be created in the absence of experimental data by invoking ideal stereochemistry, as specified in the parameter file. This can also be done for proteins for which limited data exist, e.g., if only the C$_\alpha$ coordinates are known to within 1 Å or so.