27.1. Directive IEND

Directive IEND is always required. Users may need to consider directives KWIK, LEAU, MOVE, NPLA and POSI. TOPX .... BOTZ can be very helpful. NETA is required if the Target contains ATOMS and HETATMS. The name of the Probe is usually defined in the Directive list. The remaining Directives can be ignored at first by new Users.

27.2. Other directives for GRID

The other directives for GRID are of three types which control:

1. the input/output Channels and

2. some other disposable constants which influence the way that the Programme runs and

3. the choice of Probe

Default values are provided for (1) and (2) and it may not be necessary to use any of these directives except IEND. For example, directive DWAT defines the dielectric constant of the solvent environment around the Target molecule. The default value of DWAT is 80 which is the value for water and is often appropriate for biological systems. You can reset the value of DWAT at run time by using a directive as described below.

Please note that the lineprinter output directive (LONT) should be defined first in Command Files (eg: grid.in) for Unix systems. LONT should be defined before any other directives. Apart from this restriction, the directives may be input in any sequence. Directives may be entered in small or CAPITAL letters.

There are several alternative ways of defining a Probe. The recommended method is to include a Probe symbol in the list of Directives as indicated in item (3) above.

IEND must always appear on a line by itself after all the other directives. If no directives are used, IEND must still be input immediately before the job title, to show that the computation may begin (See Section K.6).

27.3. Directives controlling input/output channels

The directives controlling the input/output channels at run time are described above. The channel assignments are made by using each four-letter keyword once or twice. It should be used first to alter the channel number if that is necessary, and then used again to define the name of the associated file thus:

This would have the effect of directing input file GRINKOUT.DAT to channel 9 instead of the default value for INPT which is 10. The other files will use their default channels. The channel number (eg: INPT 9) must precede the line with the corresponding file name (INPT GRINKOUT.DAT) as shown.

The name of the file itself must be less than 50 characters, so this line would be acceptable:

inpt /disk11/usr/annabelinda/september98/kout/hba.kout

and this line would not:

inpt /disk11/usr/annabelinda/september98/kout/hba1c.kout

On Unix systems the assignment of the lineprinter file (ie: gridlont) should come first before the other assignments. This causes the lineprinter file to be opened at the start of the run, so that it is available for messages from the very beginning.

The overall procedure for running a job by this method is therefore:

1. Make sure that the names of your input and output files cannot be mistaken for numbers. If you use 13 as a file name, then Programme GRID will think it is a channel number and will get confused!

2. Start the run. The Programme will expect file assignments and directives to be input through channel IDIR;

3. Provide paired directives in the Command File "grid.in" for every input and output file as necessary; i.e. upto eight directives in all:

   LONT gridlont.dat INPT 9 INPT grinkout.dat KONT gridkont.dat

   This would have the effect of assigning each file except GRINKOUT.DAT to its default channel. GRINKOUT.DAT will use channel 9 instead of its default channel 10. Remember that the name of each file must be less than 50 characters.

4. Continue with any more directives which may be needed (See below). All the other directives require numerical values, and not filenames. They should be entered one after the other like this: LEVL 3

5. Enter the symbol which defines the Probe that you want.

6. Finish the directive list with IEND on a line by itself.

7. Continue with the job title and the two input Parameters that determine which GRID Planes you want to study (See below).

8. Enter the Energy Variables which define the properties of the Probe, if you have not already defined your Probe by a symbol as described above. The Energy Variables are not shown in Section K.6, since the Probe is defined by its symbol OH2.

phenol 
phenolate 
pyridine

LONT gridlont.dat
INPT 9
INPT file.list
KONT gridkont.dat