Using grid (GRID)

Introduction

The program GRID (and its pre-program GRIN) is written by Peter Goodford.

This program can be used in conjunction with WHAT IF. If you type GRID, you enter a menu from which you can run GRIN, and GRID. An extensive description of these programs can be found in the GRIN/GRID writeup. The GRID menu in WHAT IF allows you to create, edit, and execute the command files needed for GRIN and GRID execution. Both GRIN and GRID can only run in batch; WHAT IF will do the submitting for you. The command MANUAL is added to the GRID menu to allow for the execution of GREAT. GREAT is a teacher that teaches you how to use GRIN/GRID properly. This can be handy, as WHAT IF will ONLY DO THE VERY BASIC THINGS for you.

GREAT allows you (only on the VAX if used via WHAT IF) via a large amount of small (interactive) menu's written by the program GREAT.EXE to generate command files (DCL-files) which then will be executed automatically.
You can of course only use GRIN/GRID/GREAT if you have gotten it from Molecular Discovery Limited. See the appendices for address etc.

Set the GRIN/GRID parameters (PARAMS)

The command PARAMS can be used to change the input parameters for the program GRIN/GRID which WHAT IF writes for you in the files GRIN.COM and GRID.COM. You can of course always change these parameters afterwards with the EDTGRN/EDTGRD command, but PARAMS gives a little bit of help about the parameters that you can change. Also, this way you will not accidentally change a parameter such that it will be impossible for WHAT IF to continue.

Using GRIN before using GRID

The following options are essential for GRIN. GRIN is the pre-processor for GRID. Without GRIN, GRID will not work.

Prepare for GRIN (MAKGRN)

The option MAKGRN will create the file GRIN.COM. This file has to be used to run the program GRIN. GRIN is the pre-processor that takes a PDB file, checks it, corrects it, and adds the energy parameters to it, thus preparing it as a proper input file for GRID.

You can either change GRIN parameters by using the EDTGRN command, which gets GRIN.COM into the edittor for you, or by setting the parameters with the PARAMS command just prior to execution of the MAKGRN command.

Inspect GRIN parameters before the run (EDTGRN)

The command EDTGRN will bring the file GRIN.COM into the edittor for you. This way an experienced user can have a last check whether he or she likes what GRIN is going to do.

Run GRIN (RUNGRN)

The command RUNGRN will cause WHAT IF to submit GRIN.COM to batch. GRIN does not take too much CPU time so you normally can wait for the result to come back.

List the GRIN results (LSTGRN)

The command LSTGRN will cause WHAT IF to show the results of the execution of GRIN at the terminal. I suggest that you look carefully at this output the first couple of times you use GRIN/GRID.

Running GRID

The following options are essential for GRID. GRID is the actual workhorse of the pair GRIN/GRID. GRIN has to run first in order for GRID to execute.

Prepare for running GRID (MAKGRD)

The option MAKGRD will create the file GRID.COM. This file has to be used to run the program GRID. GRID takes the pre-processed (by GRIN) PDB file (called PDB.PDB), and calculates a potential energy map for the requested probe.

You can either change GRID parameters by using the EDTGRD command, which gets GRID.COM in the edittor for you, or by setting the parameters with the PARAMS command just prior to execution of the MAKGRD command.

Inspect GRID parameters before the run (EDTGRD)

The command EDTGRD will bring the file GRID.COM in the edittor for you. This way an experienced user can have a last check whether he or she likes what GRID is going to do.

Run GRID (RUNGRD)

The command RUNGRD will cause WHAT IF to submit GRID.COM to batch. GRID often takes a lot of CPU time, so you normally can not wait for the results to come back. Therefore the option SAVMAP (see also SAVMAP in the MAP menu) can be used. SAVMAP saves the present map-related parameters in a file. In a next session you can use RESMAP (see RESMAP below, and RESMAP in the MAP menu) to reset the map parameters before reading the GRID map with the GETGRD command.

This somewhat user unfriendly process is needed to keep the GRID and WHAT IF parameters synchronized.

List the GRID results (LSTGRD)

The command LSTGRD will cause WHAT IF to show the results of the execution of GRID at the terminal. I suggest that you look carefully at this every time you use GRIN/GRID for a new project.

Read the GRID map in (GETGRD)

The command GETGRD will read a GRID output map. Since GRID output maps are not self contained (they have no header information), WHAT IF has to keep track of the additional information that is needed for proper reading of this map. You therefore have to remember yourself which map header belongs with which grid map. Especially if you do not read the grid map in the same WHAT IF session as the one in which you used RUNGRD, you should use the SAVMAP command in the MAP menu. If you later use RESMAP in the MAP menu to restore all map information, you should also make the GRID map you want to read the default map before using GETGRD (see DEFMAP in the MAP menu).

Saving the map header (SAVMAP)

The command SAVMAP will cause WHAT IF to prompt you for the name of a save file. It will then write all internal information about its maps in this file. This is especially handy if you want to submit GRID in one session, and want to read the GRID map in another session.

This option is identical with the SAVMAP option in the MAP menu.

Restoring saved map information (RESMAP)

The command RESMAP will cause WHAT IF to prompt you for the name of thje save file. It will then restore the internal map information from this save file.

This command is identical with the command RESMAP in the MAP menu.

Installation

It is rather easy to install GRIN/GRID for usage with WHAT IF. Just read all files from the GRIN/GRID distribution tape, and put them in the WHAT IF sub-directory /dbdata/grid. Rename the files such that they are capitalized and get a three letter extension as described below. The following is the list of the files minimally needed on my system: 

/usr2/people/vriend/whatif/grid
GRID.EXE
GRIN.EXE
GRUB.DAT
PROBES.PRO
On unix systems you will have to rename the executables as follows: grin -> GRIN.EXE, grid -> GRID.EXE. Also, the datafiles as mentioned above should be called GRUB.DAT and PROBES.PRO (the capitals are important). On unix systems the files should be present in the directory .../vriend/grid.

To run GREAT, several other files are needed. I suggest that you, if you want to use GREAT from WHAT IF, keep all files from the distribution tape in this directory, or at most delete only the writeup. Be aware however that WHAT IF can NOT read maps that are created by GRID as the result of usage of GREAT.
Be sure that you have the file PROBES.PRO in the new format which looks like: 
                                                                       

         Initial Table of Sample Probes for Programme GRID.
         --------------------------------------------------

  C1=  1.90  6.  2.07  0.000  0.00 0.00 00 00  00  Aromatic CH group
  C2   1.90  7.  1.77  0.000  0.00 0.00 00 00  00  Methylene CH2 group
  C3   1.95  8.  2.17  0.000  0.00 0.00 00 00  00  Methyl CH3 group

  N:   1.65  6.  1.10  0.000 -2.00 1.60 00 01  97  Nitrogen atom with lone pair
  N1   1.65  7.  1.40 -0.080 -2.00 1.60 01 00  01  Amide NH group
  N1=  1.65  7.  1.80  0.660 -2.00 1.60 01 00  01  sp2 cationic NH group
  N1:  1.65  7.  1.40  0.000 -2.00 1.60 01 01  51  sp3 NH group with lone pair
  N1+  1.65  7.  1.40  0.660 -2.00 1.60 01 00  31  sp3 NH cation
  N2   1.70  8.  1.70  0.000 -2.00 1.60 02 00  02  Amide NH2 group
  N2=  1.70  8.  2.10  0.660 -2.00 1.60 02 00  02  sp2 cationic NH2 group
  N2+  1.70  8.  1.70  0.660 -2.00 1.60 02 00  22  sp3 cationic NH2 group
  N3+  1.75  9.  2.13  0.660 -2.00 1.60 03 00  03  sp3 cationic NH3 group

  OC2  1.60  6.  0.64 -0.200 -1.50 1.50 00 02  28  Ether oxygen atom
  OES  1.60  6.  0.64 -0.200  0.00 0.00 00 00  00  Ester oxygen atom
  O    1.60  6.  0.84 -0.250 -4.00 1.40 00 02  08  Carbonyl oxygen atom
  O::  1.60  6.  2.14 -0.450 -4.00 1.40 00 02  08  Carboxy oxygen atom
  ON   1.60  6.  2.14 -0.100 -4.00 1.40 00 02  08  Nitro oxygen atom
  O=   1.60  6.  2.14 -0.400 -4.00 1.40 00 02  64  Phosphate oxygen atom
  O-   1.60  6.  2.14 -0.500 -4.00 1.40 00 02  88  Anionic phenolate oxygen atom
  O1   1.65  7.  1.20 -0.100 -4.00 1.40 01 02  04  Aliphatic hydroxyl group
  OH   1.65  7.  1.50 -0.150 -4.00 1.40 01 01  34  Phenolic hydroxyl group

  F    1.45  8.  0.40 -0.300  0.00 0.00 00 00  00  Fluorine atom
  F-   1.36  9.  0.80 -1.000  0.00 0.00 00 00  00  Fluoride anion
 CL    1.80 12.  2.80 -0.250  0.00 0.00 00 00  00  Chlorine atom
 CL-   1.81 13.  2.90 -1.000  0.00 0.00 00 00  00  Chloride ion
 BR    1.95 22.  3.40 -0.200  0.00 0.00 00 00  00  Bromine atom
 BR-   1.95 22.  4.20 -1.000  0.00 0.00 00 00  00  Bromide ion
  I    2.15 30.  5.40 -0.100  0.00 0.00 00 00  00  Iodine atom
  K+   1.33 16.  1.93  1.000  0.00 0.00 00 00  00  Potassium cation
 NA+   0.95  8.  0.24  1.000  0.00 0.00 00 00  00  Sodium cation
  PO4H 2.30 24.  6.20 -1.000 -4.00 2.30 01 07  00  Complete PO4H phosphate anion
  PO4  2.30 24.  6.20 -2.000 -4.00 2.30 00 08  00  Complete PO4 dianion

  OH2  1.70  7.  1.20  0.000 -4.00 1.40 02 02  95  Water
WHAT IF reads the probe data from this file. So any new probes you want to define (or use) should also be present in this file.