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I. A Description of the Structure

The Protein Structure File (CHARMM: `.psf') contains a description of all molecules in the system to be simulated, their covalent connectivity, and all the energetic interactions to be calculated. Despite its name, the psf is not limited to proteins. It may be used to describe other systems, such as nucleic acids or lipids. The psf defining a specific system (e.g., carboxymyoglobin (MbCO) hydrated by 350 water molecules) is assembled, or GENErated, from the generic building blocks defined in the Residue Topology File (.rtf). To generate the psf for hydrated MbCO, we need amino acids and water molecules (defined in aminoh.rtf), and a heme and CO ligand (in porphyrinh.rtf). Again, despite the term `rtf', the components found in an rtf need not be amino acid residues. Other rtf's contain different building blocks: base pairs, lipid head groups, etc.

Peter J. Steinbach 2010-11-15