If this variable is present, the program tries to read the atomic coordinates from the file specified by its value. The PDB (Protein Data Bank) format is quite complicated, and it goes well beyond the scope of this manual. You can find a comprehensive description here. From the plethora of instructions defined in the PDB standard, Octopus only reads two, ATOM and HETATOM. From these fields, it reads:
- columns 13-16: The species; in fact Octopus only cares about the first letter - CA and CB will both refer to carbon - so elements whose chemical symbol has more than one letter cannot be represented in this way. So, if you want to run mercury (Hg), please use one of the other methods to input the coordinates.
- columns 18-21: The residue. Ignored.
- columns 31-54: The Cartesian coordinates. The Fortran format is (3f8.3).
- columns 61-65: Classical charge of the atom. Required if reading classical atoms, ignored otherwise. The Fortran format is (f6.2).
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