7.1. Small molecule mode

Extended Atoms are not used for small molecule Targets. All the Target atoms including hydrogens are considered, but it is not essential for the User to supply all the hydrogen coordinates in the PDB input file. Such coordinates will be used if they were supplied, but standard coordinates will be calculated by Programme GRIN if the observed hydrogen positions were not provided. GRIN does this automatically, using the name of the heavy atom as a cue to the hydrogen positions, and the whole process should be transparent to the User.

The atoms of a small molecule Target are treated as HETATMS, according to the conventions of the Brookhaven Data Bank. The appropriate HETATM variables will be selected by Programme GRIN from the HET section at the end of datafile GRUB. Correct atom names must therefore be assigned to each HETATM in the PDB file for the small molecule, so that they will correspond with the names in GRUB.

Programme GREAT will assign most HETATM names in an organic molecule automatically. It gives each atom the appropriate name for use in Grid calculations, and GREAT also contains an editor which can be used in order to rename any outstanding ATOMS or HETATMS that were not dealt with automatically. It can also convert other input formats into Brookhaven (PDB) Data Bank Format, and the overall procedure for this is summarised in Diagrams 2 above and 3 below.

7.2. Macromolecule mode

For macromolecules the atoms are generally grouped as Extended Atoms into residues. For example the amino-acid glycine in a protein would be treated as the residue: -NH-CH2-CO- and the -CH2- moiety in this residue would be treated as an extended atom. Each extended atom is treated as a single ATOM, and its Energy Variables are selected by Programme GRIN from the appropriate section of datafile GRUB. There is, for example, a section called: GLY in datafile GRUB with Energy Variables for the glycine residue.

7.3. Mixed mode

This Mode is used when your original PDB input file contains both ATOMS and HETATMS. In this case it is essential to list all the HETATMS after the list of ATOMS in the PDB file. The ATOMS and HETATMS must not be mixed up, or the PDB file will not be acceptable as input for Programme GRIN. The correct ATOM>HETATM sequence is arranged automatically when the input is prepared by Programme GREAT.

With Mixed Mode it may be necessary to set NETA and some of the other GRID directives, as described under Programme GRID below.

7.4. Set mode

Programmes GREAT, GRIN and GRID can process a set of several different Targets one after the other in the same run. The set of Targets is called a "Set", and the procedure is described below (See Index under Set of Targets). However, we recommend that New Users first run the Programmes with one single Target at the time, before trying to use a Set of Targets all together.

>DIAGRAM 3:  PROCEDURE FOR DEALING WITH UNUSUAL FILE FORMATS