11.1. Atoms in datafile GRUB

Datafile GRUB is arranged in two main parts. It begins with specific variables for ATOMS in Recognised Molecules. Each Recognised Molecule is identified by a three character code. They are arranged in alphabetical sequence so that Alanine, for example, is near the head of the list. Its three character code is ALA, and variables are provided for the atoms:

N  CA  C  O  CB

of an alanine molecule, and for OXT in case the alanine is a residue at the carboxy terminus of a protein sequence. Programme GRIN will only use the OXT value if the last ATOM record of the alanine is followed by a TER record, which shows that it is the carboxy terminal of a protein. (Note that some crystallographers omit the OXT atom from their PDB files altogether, or give it another name, or omit the TER card).

If the Recognised Molecule is not an amino-acid, no OXT energy variables are needed.

The alanine variables for N C and O refer to individual atoms. However, CA and CB are extended atoms, and these symbols refer to the whole alpha-carbon CH group and the whole beta-carbon CH3 group of alanine respectively.

If the Target contains an Unknown Molecule, whose molecule name does not correspond to one of the three-character molecule names in GRUB, the Energy Variables of its ATOMS will still be taken from the list of Recognised Molecules in GRUB. See the Section on Unknown Molecules below.

11.2. Hetatms in datafile GRUB

The final part of datafile GRUB deals with Energy Variables for different types of HETATM. These are listed under the heading HET at the end of datafile GRUB, and are assigned to records in the PDB file which begin with the letters 'HETATM'.

Programme GRIN merges datafile GRUB with a PDB file of coordinates. When this merge takes place, each molecule in the PDB file is assigned to one of three classes:

>1. RECOGNISED MOLECULES

These are molecules which may occur frequently in the Target, such as the common amino-acids. A recognised three-character name (Variable ACID) will already have been assigned to such a molecule, and there will already be Energy Variables for its ATOMS in datafile GRUB. They will be listed under the ACID and ATOM name. These are the "Recognised Molecules", and the corresponding records in the PDB file must begin with the six characters 'ATOM '.

>2. UNKNOWN MOLECULES

If the PDB atom is not in a "Recognised Molecule", then the name (ACID) of that molecule will not occur in datafile GRUB. The compound will have some other three character name, and will be treated as an "Unknown Molecule" so long as the PDB records still begin with the six characters: 'ATOM '.

The Energy Variables for ATOMS in an "Unknown Molecule" will still be taken from the first part of datafile GRUB; i.e. the part devoted to ATOMS in "Recognised Molecules". However, they will be selected from the first ATOM in datafile GRUB which has the same ATOM name, irrespective of the actual molecule name in GRUB. This may not be inappropriate for compounds of similar type to the Recognised Molecules, such as a less-common amino-acid. However, it is a default fall-back procedure and should never be used intentionally.

>3. HETERO MOLECULES

If the PDB record begins with the six characters 'HETATM' then the variables will be taken from the final section of datafile GRUB. The actual name of the molecule is largely irrevelant in this case. However, each Hetero-molecule must be given a name and number which distinguish it from the other Hetero-molecules. Programme GREAT will assign the names MOL1 MOL2 etc to Hetero-molecules automatically, or allow the User to supply preferred names.

Some of the checks applied by Programme GRIN to the original PDB file can only be applied to "Recognised Molecules". For example the ATOMS of a "Recognised Molecule" will be rearranged into a standard sequence which is defined by the sequence of ATOMS in datafile GRUB, but this cannot be done for "Unknown Molecules" or for the HETATMS in a "Hetero-Molecule".