GRID manual
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Chapter 20. Directives for programme GRIN

The default values are normally acceptable for all the directives used by GRIN. Most Users do not need to alter any of them, but this Section describes how to do so if the need arises.

The directives for GRIN control:

the input/output channels
some other disposable constants which influence the results and the way that the programme runs.

The default values are defined at the start of the Programme. For example the default value for directive EFHY is 1.0, which is normally an acceptable value for the number of electrons on a hydrogen atom! If you want to change the default value of EFHY for some reason you can use a directive at run time as described below.

IEND must always be the last directive, when you are setting up a run with Programme GRIN. The lineprinter output directive (LOUT) should always be defined first on Unix systems. Apart from these restrictions, the directives may be input in any sequence.

Directives having unreasonable values will be rejected at run time.

Directives may be entered using small or CAPITAL letters.

20.1. Directives controlling input/output channels

The channel assignments are made by using each four-letter keyword once or twice. It may be used first in order to alter the channel number if that is necessary, and then used again to define the name of the associated file thus:

  LOUT grinlout.dat
  KOUT grinkout.dat
  INAT 9
  INAT grub.dat
  INKO pdb.pdb

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

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

inko /disk1/usr/marmaduke/brookhaven/proteins/hba.pdb

and this line would not:

inko /disk9/usr/marmaduke/brookhaven/proteins/hba1c.pdb

On Unix systems the assignment of the lineprinter file (i.e.: grinlout) 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 the Second method is therefore:

Make certain that channel IDIR has an acceptable number for your computer system. The value is normally IDIR=5 when the programme is supplied, and this is usually acceptable.
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 GRIN will think it is a channel number and will get confused!
Start the run. The programme will expect file assignments and directives to be input through channel IDIR; i.e. channel 5 by default, unless you edited it in item (1) above.
Provide directives in the Command File "grin.in" for every input and output file as necessary; i.e. upto eight directives in all:
LOUT grinlout.dat KOUT grinkout.dat INAT 9 INAT grub.dat INKO pdb.pdb
This would have the effect of assigning each file except grub.dat to its default channel. Grub.dat would be assigned to channel 9 instead of its default channel 10. Moreover, you could use other channel numbers for all the files just as easily. Remember that the name of each file must be less than 50 characters.
Continue with any other directives (e.g. IHVA or LEVL; see below) which you need. Just enter each Directive and its numerical value thus:
LEVL 3
and finish the directive list with IEND on a line by itself. (IEND does not need any numerical value)

20.1.1. Inputting a file list

In the above examples the primary input was a single file called PDB.PDB. Alternatively you may prepare a file (which we will call FILE.LIST) containing a list of file names. Each of the files in the list will then be processed one after the other as a Set.

There is no limitation to the number of Target molecules in a FILE.LIST for Programme GRIN, but each file-name must be less than 50 characters long. This character count includes the suffix .kout and so the name on each line of the file list should be less than 45 characters. It is also worth remembering that the maximum number of Targets in a FILE.LIST for Programme GRID is 1500.

The name of each Target must appear on a separate line of FILE.LIST thus:

  phenol 
  phenolate 
  pyridine

and the input directions by would then be:

  LOUT grinlout.dat        (Small letters would                     
  INAT 9                    normally be used for                    
  INAT grub.dat             the file names on a                     
  INKO file.list            Unix style system)

This would cause programme GRIN to make three successive runs, processing phenol.pdb to give phenol.kout; phenolate.pdb to give phenolate.kout and pyridine.pdb to give pyridine.kout.

Note that no suffixes are required for the names in file.list.

Note also that it is not necessary to define grinkout.dat because separate .KOUT files are produced for each PDB input file. All warnings and messages go to the one Lineprinter OUTput file.

See Index under Set of Targets for more information.

Note: The following Directives ALHY EFHY IHVA IHAC LEVL MOVE QQHY and VDHY are not normally needed by Programme GRIN.

20.2. Control directives

These directives control the way in which the Programme runs. The Control Directives consist of one or more input lines in the command file, and they must follow the Channel assignments. Each four-letter directive must have an appropriate numerical value. The free format input expects integer values (no decimal point) for Directives starting with the letters I, J, K, L, M, and N. Do not use Tabs (the "TAB" character) in order to format your input.

Default values are supplied for the following directives. Users will usually find that these default values are acceptable, and so they will not normally have to use any Control Directives at all.

20.2.1. VDHY

Directive VDHY is the Van der Waals radius assigned to a hydrogen-bonding hydrogen atom, when directive IHVA has also been set. Units are Angstrom.

Default value: VDHY = 0.6

Range: 0.009 < VDHY < 2.0

20.2.2. ALHY

Directive ALHY is the polarizability (alpha) assigned to a hydrogen-bonding hydrogen atom, when directive IHVA has also been set. Units are Angstrom to the power 3.

Default value: ALHY = 0.04

Range 0.01 < ALHY < 2.0

20.2.3. EFHY

Directive EFHY is the number of electrons assigned to a hydrogen-bonding hydrogen atom, when directive IHVA has also been set. It determines the strength of the Van der Waals interaction.

Default value: EFHY = 1.0

Range: 0.1 < EFHY < 9.0

20.2.4. QQHY

Directive QQHY is the electrostatic charge assigned to a hydrogen-bonding hydrogen atom, when directive IHVA has also been set. Units are the charge on the electron (with changed sign).

Default value: QQHY = 0.0

Range: -9.5 < QQHY < 9.5

20.2.5. IHVA

Directive IHVA determines whether Lennard-Jones variables and electrostatic charges will be assigned to the hydrogen-bonding hydrogen atoms which are bonded to ATOMS. This directive does NOT effect hydrogens which cannot form hydrogen-bonds. It does NOT effect hydrogens which are bonded to HETATMS, because those hydrogens are always explicitly treated. Its effect is summarised in diagram 4 below. When IHVA=0 (the default value) the hydrogen-bonding hydrogens bonded to ATOMS will not be assigned Lennard-Jones variables and electrostatic charges. These hydrogens, which are normally in macromolecules, are mainly used as pointers for the direction of hydrogen-bonds. However, if IHVA=1 then the values ALHY, EFHY, QQHY and VDHY will be assigned to every hydrogen-bonding hydrogen which is bonded to an ATOM.

Default value: IHVA = 0

Range: IHVA = 0 or 1

Note: In summary, the default value of IHVA is usually appropriate for small molecules composed of HETATMS, and is also appropriate for macromolecules composed of ATOMS. It is, therefore, normally transparent to the User.

Note that:

Hydrogens in macromolecules are not explicitly considered if they do not form hydrogen-bonds. Ordinary hydrogens are grouped together with their heavy atom to form an Extended Atom.
On the other hand, all the hydrogens on HETATMS are treated explicitly. If a hydrogen in a hetero-molecule does not form hydrogen bonds, it is assigned Energy Variables from the hydrogen entry in the last (HET) section of datafile GRUB. If it forms hydrogen bonds, it is assigned values ALHY, EFHY and VDHY.
Saunderson's method is used to compute the charges of all the hydrogens bonded to HETATMS in hetero-molecules. QQHY defines the charge of hydrogen-bonding hydrogens bonded to ATOMS in macromolecules.

Diagram 4: The treatment of hydrogens

20.2.6. IHAC

Directive IHAC controls the charge assignment method. With the default value (IHAC=0) the Saunderson's algorithm is applied, whereas when IHAC=1 a semiempirical method is used.

Default value: IHAC = 0

Alternative value: IHAC = 1

Note: This Directive has been implemented only in the Programme GREATER. All Users who are more practice using GREAT may manually add a line in the command file GRIN.IN.

20.2.7. ALMD

Directive ALMD determines whether extra information is written by GRID to the GRIDKONT output file.

Default value: ALMD = 0

Range 0 < ALMD < 1.0

20.2.8. LEVL

Directive LEVL controls the amount of information printed in GRINLOUT by the line printer. Bigger values give more information.

Default value: LEVL = 2

Range: -2 < LEVL < 6

20.2.9. MOVE

Directive MOVE controls the amount of information printed in GRINKOUT. In Programme GRIN it may only take the value 0 or 1. When MOVE=1 the Programme takes longer to run, but calculates all the extra information which will be needed by GRID in order to take account of conformational flexibility in the Target. When MOVE=0 in GRIN this extra information is not computed. The default value is MOVE=1 and this is recommended. However, some Users with old slow systems may want to set MOVE=0.

Default value: MOVE = 1

Alternative value: MOVE = 0

20.2.10. IEND

Directive IEND is used to on a line by itself after any other directives, to show that the list of directives has finished. No numerical value is given to IEND.

Note: Directive IEND must always appear on a line by itself after all the other directives. If no directives are used, IEND must still be input to show that the computation may begin.

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