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Chapter 26. User guide to programme GRID
26.1. Structure of programme GRID
The relationships between Files and Programmes are shown in Figure 2.
Programme GRID requires one input file (GRINKOUT); a set of input Directives; and some input Parameters.
GRID produces two output files: GRIDLONT is the lineprinter output with tabulated results, and GRIDKONT is the computer-readable output file.
26.2. Programme modes
Programmes GREAT, GRIN and GRID may be used in one of four different Modes known as:
Small Molecule Mode
Macromolecule Mode
Mixed Mode
Set Mode
In Small Molecule Mode the Target is all composed of HETATMS. In Macromolecule Mode the Target is all composed of ATOMS. In Mixed Mode both ATOMS and HETATMS are present in the Target. In Set Mode one may study a Set of Targets one after the other.
The distinction between ATOMS and HETATMS has been described above (see under Atom Name Conventions). The Modes have also been described, but Mixed Mode will now be considered in greater detail.
26.2.1. Mixed mode
Mixed Mode is used when the original input PDB file contains both ATOMS and HETATMS. In this case it is essential that all the HETATMS be listed after the ATOMS in the PDB file. If necessary, the PDB file must be edited, before using the previous Programme GRIN, so that all the HETATMS come after the ATOMS.
Directive NETA controls the number of HETATMS which will be included with the ATOMS in order to make up the complete Target in Mixed Mode. NETA is normally assigned an appropriate default value automatically in Small Molecule Mode; in Macromolecule Mode; and in Set Mode. However, it has the default NETA=0 in Mixed Mode (ie: when ATOMS and HETATMS are both present), and the Target will then consist of all the ATOMS and none of the HETATMS.
If the User wants some of the HETATMS to be included with the ATOMS of the Target in Mixed Mode, he or she must define the exact number required. This is done by setting an appropriate value for directive NETA as described in detail below.
An alternative approach in Mixed Mode is to set NETA to a large positive value which will bring all the HETATMS into the Target. Unwanted HETATMS can then be eliminated by using crosses as described under Programme GRIN above. The explicit symbol to be used for the cross is a CAPITAL X LET: X ATOMS and HETATMS for which variable IHET(I) has the value XLETA are "crossed out", which means that they will be completely ignored by Programme GRID.
NETA is automatically set to a large positive value, when several Targets are being studied together as a Set. This exception to the normal default situation should be carefully noted. See the Special Note below under Message D515.
Click here for detailed information about NETA.
26.3. Input and output channels
Five "Logical Units" are used by Programme GRID. These are numbered Channels through which data, results, and other information enter and leave the Programme as shown in Figure 2. One is used for input of the GRINKOUT file that has previously been prepared by Programme GRIN (This is the file with the details of the Target). Two more are for the output files GRIDLONT and GRIDKONT. The fourth channel is for the command file grid.in with the Directives for GRID.
The correct use of input and output channels with various operating systems is described in more detail below.
26.4. Input to programme GRID
Input consists of three components:
the file GRINKOUT
the Directives
some Parameters
File GRINKOUT must be previously prepared by Programme GRIN (see above) and is input through Channel INPT. As mentioned above, a list of file names may be input through Channel INPT instead of one single GRINKOUT file. See under Set of Targets or see below under the heading STUDYING A SET OF TARGETS for more information about this alternative procedure.
The Directives and Parameters are input through Channel IDIR as shown in Figures 2 and 7. Each directive must appear on a line by itself. They are input successively, and finish with the obligatory directive IEND which comes before the job title.
26.4.1. The input file GRINKOUT
GRINKOUT is prepared by the previous Programme GRIN, and is fully described in the documentation for that Programme (see GRINKOUT). GRINKOUT is input to this Programme GRID through channel INPT. Normal default value INPT=10
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