Chapter 8. Extended Atoms
There are two important exceptions to the use of Extended
Atoms in Macromolecule Mode. Both exceptions are transparent to the
User, but they must be mentioned. First, many atoms do not bear
hydrogens and so the question of an extended atom does not arise.
For example carbonyl carbon is just one atom, and so is carbonyl
oxygen. Second, in macromolecule Mode the coordinates of
Hydrogen-bonding hydrogen atoms will always be computed by
Programme GRIN, and will be separately listed at the end of the
output file GRINKOUT. This allows their positions to be explicitly
considered when the hydrogen-bonding computations are
performed.
| Warning about ATOMS and HETATMS |
If a PDB file contains both ATOMS and HETATMS, then the
HETATMS must be listed after the ATOMS. Programme GREAT will
arrange the records automatically. Otherwise, you can use a line
editor to rearrange the sequence of records in the PDB file, before
you use it as input for Programme GRIN. |