31.1. The job title for the Grid run

The first line of parameter input is a job title of upto 80 characters. This line comes immediately after the line with IEND. A title must be supplied in order to satisfy the free-format input; i.e. this line must not be omitted, although it can be left blank. Do not use tabs.

31.2. The Z-plane parameters

The second line of Parameter input permits the User to divide a large Grid into smaller slices. For example, with a really big Target you might want to compute half of the Grid on Monday night, and the rest on the following evening. You would do this as follows.

All Grid calculations are performed step by step, and each step of the calculation deals with the GRID Points on a single plane which is perpendicular to the z-axis. The planes stack up to encompass the whole Target like slices in a loaf of bread. They are called z-planes, and sucessive z-planes are numbered along the z-axis from unity upto an upper limit which depends on CLER, NPLA and the dimensions of the macromolecule. The second line of parameter input must contain two positive integers NZ1 and NZ2 defining the particular z-planes of which are to be calculated.

A special situation arises if NZ1=0. In this case ALL the z-planes will be computed, and any value may be used for NZ2. It is conventional to use NZ2=1 in this case, so that the second line of parameter input becomes:

    0  1

This procedure (with values 0 and 1) is normally used unless the Target is very big, or the grid points are very close together (NPLA > 3). It should always be used if a small Grid cage has been defined by setting TOPX ...BOTZ. The values 0 and 1 must always be used, so that all z-planes are calculated, if the results from Grid are to be used as input for Programme Group.

On the other hand, if you were using a particularly big Target and therefore wanted to do a batch of z-planes each night, you might start with the values 1 and 120 on Monday; 121 and 240 on Tuesday; 241 and 360 on Wednesday and so on. You would do 120 planes each night, and could merge the files to give the final (enormous) Grid map.

In a situation like this it is often appropriate to rotate the Target before starting the computation. For example, a long molecule such as collagen should be rotated so that its greatest length is parallel to the z-axis. Then you can have any number of z-planes, although the dimensions in x and y would still be limited by the parameter MAXGRD (for more information see Message D475 below).

Note that it is always necessary to input two integer values (NZ1 and NZ2) on this second line of parameters, in order to satisfy the free-format input for GRID. A dummy value for NZ2 is still needed if NZ1=0, and in this case the values 0 and 1 are conventionly used as described above. Do not use Tabs.

Also note that NZ1 must not exceed NZ2.

31.3. The energy variables for the probe

The third parameter line provides a very flexible method of inputting the Energy Variables for a Single-Atom Probe, because the User can specify any physically meaningful value for each Energy Variable. However this method may not be used if:

• The properties of the Probe have been defined by a Symbol in the Directive LIST, as described above, or

• A multi-atom Probe is being used.

The recommended method of selecting a Grid Probe is always by including its Symbol before IEND in the list of Directives, but there is an alternative method for Single Atom Probes whose explicit properties may be defined on a third line of Parameter input. This line may contain eight (or nine) free-format numbers which are the appropriate Energy Variables for the Single Atom Probe. The third line is optional. It should not include tabs (the "TAB" character), and must be omitted altogether if the Probe has been chosen by one of the other methods.

The individual Energy Variables for a single-atom Probe will now be considered. They must always be entered on one line in the correct sequence. The same Variables (except JTYPE) are also used to define the individual atoms of a multi-atom Probe. These Energy Variables are:

• VDWRJ is the Van der Waals radius of the Probe in Angstrom. The suffix J indicates that this Energy Variable (and the remaining seven (or eight) variables below) all relate to the Probe. VDWRJ is a real number.

• NEFFJ (INTGER) is a factor which has been described as the number of effective electrons surrounding the Probe. In early Versions of the Programmes (before Version 15) a real variable EFFNJ was used, but the number of electrons must be an integer and NEFFJ is the name for an integer under the Fortran-77 convention.

• ALPHJ (real) is the polarizability of the Probe. Units are Angstrom to the power 3.

• QJ (real) is the electrostatic charge on the Probe. Units are the electron charge (with changed sign).

• EMINJ (real) is the energy value at the energy minimum of the hydrogen bond function

• EHB = C/(d**8) - D/(d**6)

  in which d is the distance between the heavy atoms engaged in hydrogen-bonding; e.g.the N....O distance for an N-H..O hydrogen bond. Units are Kcal/Mole.

• RMINJ (real) is the hydrogen-bonding radius of the Probe, corresponding to the hydrogen bonding radius RMIN(I) of the hydrogen-bonding heavy atom in the Target molecule. The sum (RMINJ + RMIN(I)) is equal to the distance d between the heavy atoms at the energy minimum of the hydrogen-bonding function. Note that these radii are assigned to the heavy atoms or extended atoms engaged in hydrogen bonding, not to the hydrogen atom itself. Units are Angstrom.

• JD (integer) is the maximum number of hydrogen bonds which the Probe group can donate (-1 < JD < 10). If JD > 4 the rate of calculation may be significantly reduced.

• JA (integer) is the maximum number of hydrogen bonds which the Probe group can accept (-1 < JA < 10). If JA > 4 the rate of calculation may be significantly reduced.

• JTYPE (integer) is the hydrogen bonding Type of the Probe. It must be given for the Hydrophobic and Amphipathic Probes, but is otherwise optional and may be omitted. If JTYPE is absent, then no account will be taken of the angles at the Probe made by its own hydrogen bonds. For instance, an sp2 amide NH2 Probe tends to make two hydrogen bonds subtending an angle of 120 degrees at the Probe. However, this angle will only be considered during the computation, if an appropriate value of JTYPE is provided. Note that the Probe must be able to make at least two hydrogen bonds, for JTYPE to have any meaning. It is not necessary nor it is appropriate to assign a JTYPE value to a Probe which only makes one hydrogen bond, or which makes none at all. JTYPE is not used for multi-atom Probes, because a different procedure is used to define the hydrogen bond geometry in that case. On the other hand JTYPE is used to define the properties of metal cation Probes, but this is a special application of this variable If two or more hydrogen bonds can be made by a single-atom Probe, the computation will proceed more rapidly if JTYPE is omitted. However, the favoured binding sites will not be so well defined, and the use of JTYPE values is strongly recommended.

31.4. Table of JTYPE values for single-atom probes

This table shows the values of JTYPE which may be used in order to define the hydrogen-bonding geometry of single-atom Probes in this version of Programme GRID. Any other value of JTYPE will be ignored in the definition of a Probe. Each Type has been described in detail under Programme GRIN above, and is also summarised in Appendix B (the Table of Types).

Note that more than one JTYPE value may be provided for the same chemical group. Thus types 3 and 83 define the same Probe type, and so do types 4 and 84, and types 95 and 96.

Note also that the same value of JTYPE may be used for different chemical groups. In the above table type 34 is shown twice as an example of this. Type 34 can be either a phenolic or a carboxy OH group, and these two Probes would be distinguished by their other properties. The JTYPE value only defines the hydrogen-bonding geometry of the Probe.

Note finally that 91, 92 and 110-119 are JTYPE values which are used for special types of Probe.