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PDB file format

The Protein Data Bank (PDB) file format is used to store coordinate or velocity data. This is the standard format for coordinate data for many bioinformatic programs. A full description of this file format can be obtained from the PDB web site [45]. You can generate PDB files in nMOLDYN by extracting one or several frames from a MMTK trajectory file (see Section 4.1.3). PDB files are also used in nMOLDYNwhen performing subset, deuteration or group selection from a nMOLDYN selection file (see Sections 4.2.2.1, 4.2.2.2 and 4.2.2.3).