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Chapter 24. Editing Files
24.1. Editing datafile GRUB
GRUB may be edited in order to change the Energy Variables. Any of the Energy Variables VDWIN, NEFFIN, ALPHIN, QIN, EMININ, and RMININ may be changed to different reasonable values in datafile GRUB. However, the format of the table must not be altered, and it must begin with 15 lines of header followed by the actual data starting with A for ADENOSINE on line 16.
There is as yet no general agreement on the best values to use for Energy Variables, and many scientists will wish to make small changes to some of the values in Datafile GRUB. This is acceptable, but Programme GRID will reject values of VDWIN, NEFFIN, ALPHIN, QIN, EMININ, or RMININ if they are unreasonably large or small.
More care is needed if the variables IDIN or IAIN are to be changed. IDIN and IAIN are normally zero in datafile GRUB, and Programme GRIN then assigns suitable values to IDIN and IAIN from its catalogue of hydrogen bond Types . However, the User may insert reasonable values for IDIN and IAIN into GRUB, and those inserted values will then have priority over the standard values.
N1IN defines the Type of hydrogen bonds formed by an ATOM or HETATM. If the value of N1IN is changed, then the new value must satisfy several requirements. In particular, the atom must have the correct number of heavy atoms as bonded neighbours. Thus a ketone oxygen (Type 8 with one neighbour) could be changed into an hydroxyl oxygen (Type 4 with one heavy neighbour) but not into an ether oxygen (Type 28) because an ether oxygen must be bonded to two neighbouring heavy atoms.
In principle, all the Type numbers listed in the Index are acceptable, and Users are most strongly advised to use no other Type numbers.
In summary, therefore, there should be no problem if the N1IN value is edited to another EXISTING Type number, so long as it refers to an atom or hetatm which has the appropriate number of bonded neighbours.
24.1.1. Adding new lines to Grub
More Recognised Molecules may be added to datafile GRUB. Each new molecule may contain upto 199 atoms. The total number of Recognised Molecules may not exceed 199. If the Recognised Molecule is an amino-acid, the last atom should be ' OXT'.
More hetero atoms may be added under the heading 'HET' In this case the number of HET lines must be changed where it appears after the word HET, unless the default value -1 is being used. The datafile is initially supplied with the default value -1 and its use is recommended. The total number of hetero-atoms in datafile GRUB must not exceed 999. It is sometime convenient to have several different versions of GRUB, each containing different HETATMS.
If the new entry for a HETATM at the end of datafile GRUB represents an Extended Atom, it is marked with the letters 'EA' at the end of the line. In general, however, HETATM entries refer to individual HETATMS; e.g. the entry C3 is the carbon of a methyl group but NOT the extended methyl group 'in toto'.
It is the sequence of ATOM lines within a Recognised Molecule in datafile GRUB which determines the sequence in which the atoms will appear in GRINKOUT. Datafile GRUB is initially supplied with atoms in the sequence as specified for the Brookhaven Protein Data Bank. The sequence in GRUB may be altered, but this is NOT recommended.
The 'number of ATOMS' in each Recognised Molecule type appears immediately after the abbreviated molecule name in GRUB thus:
ALA 6
This number must always correspond with the number of ATOM lines immediately following. It should NOT be changed unless the number of ATOM lines for the Recognised Molecule is altered to match, and that is most unlikely to happen.
24.1.2. Removing lines from Grub
Some Users may add new Recognised Molecules and HET names to Datafile GRUB, which then becomes so large that slow computers take a significant time to read it all. In this case you may wish to edit the file again, and remove any entries which you never use yourself.
We recommend that the name GRUB.SHORT be used for this shorter file. Note that the first 15 header lines of GRUB.DAT must also be the header lines of GRUB.SHORT, without any changes. This exact Header must always be present at the start of any GRUB file, and it must then begin with ADENOSINE as the first Recognised Molecule because Programme GRIN checks for ADENOSINE in order to be sure that it is really at the start of the data.
24.2. Editing input file PDB
The PDB input file may be edited, and sometimes needs editing several times before an acceptable file GRINKOUT is obtained ready for input to Programme Grid. The original file may well contain many lines of notes and remarks and references which all generate messages to GRINLOUT when the PDB file is first used as input to Programme GRIN. All these lines may be edited out of the PDB input file with care, so that the significant warnings in GRINLOUT become more obvious when GRIN is run a second time. It may then be necessary to make further changes to PDB, and these frequently require careful and serious scientific consideration.
A Protein Data Bank File may have missing lines, if the positions of some atoms or hetatms were not well established by the X-ray observations. In this case it is usually appropriate to add extra lines to file PDB so that they correspond to the missing atoms. It will probably be necessary to study the Target structure by computer graphics in order to decide on the most appropriate positions for missing side chains. Programme GRID itself may be used in order to decide where the missing side chains should go.
Sometimes a chemical group appears twice over in a PDB file providing alternative locations for several atoms, and it is then necessary to decide which atom lines to accept and which to reject. The unacceptable lines must be deleted from the PDB file not from GRINLOUT). Another approach would be to run GRIN and GRID twice, first with one set of atom locations and then the other.
You may wish to alter the BVAL or OCCUP values of some atoms to -99.99 in order to force them into or out of the Core of the Target (See above under the heading FORCING ATOMS INTO THE CORE).
In general, a number of changes may be needed before a version of file PDB is obtained which generates an acceptable version of file GRINKOUT. Moreover, these changes may be of a kind that requires a considered scientific assessment.
24.3. Editing output file GRINKOUT
Generally speaking the GRINKOUT file should not be edited except in a very limited way for very special purposes. It is easy to make changes which give versions of GRINKOUT that do NOT run correctly with Programme GRID.
Fortunately the output from Programme GRIN gives a GRINKOUT file with the correct overall layout. This should be used as a guide if you must edit GRINKOUT. Please note that THE FORMAT OF THE GRINKOUT FILE AND THE NUMBER OF LINES IN THE FILE SHOULD NEVER BE CHANGED. THE SEQUENCE IN WHICH THE LINES ARE LISTED SHOULD NEVER BE ALTERED NOR SHOULD THE FIRST TWO NUMBERS AT THE START OF ANY LINE.
However, GRINKOUT is actually printed in ASCII so that it can be carefully checked and edited before use with Programme GRID. Three examples of editing will now be given.
24.3.1. Symmetrical targets
The 17th column of PDB format is used for the ALT marker which indicates an alternative position for an atom. However the same column of a GRINKOUT file can be used to mark symmetrical atoms in a symmetrical target (see also under KWIK with Symmetrical Targets). An exclamation mark (!) is used as a marker, and may be edited into column 17 of GRINKOUT where appropriate.
24.3.2. Changing the energy variables
There was experimental evidence that an ionisable histidine residue in a certain protein sequence had an unusual environment. The electrostatic charges listed in datafile GRUB would therefore be inappropriate for that individual residue in that particular place.
In such a situation one possible procedure might have been to edit datafile GRUB itself, altering the charges assigned to the histidine atoms. However, editing GRUB would have been inappropriate in the present case because it would have influenced the Energy Variables assigned to all the histidine residues in the whole Target protein. The electrostatic charges in the GRINKOUT file were therefore edited, for the atoms of the one particular histidine residue alone, to give a more realistic input file for Programme GRID.
It is usually acceptable to alter the Energy Variables assigned to an atom, and change them to other reasonable values. However one should not try to split the electron by altering some atom charges so that the overall charge of the Target was no longer an integer value. Care is also needed with the xyz coordinates of the atoms. Problems may arise if these are changed so that two mutually bonded atoms are an unreasonable distance apart. There may also be problems if two unbonded atoms are brought too close together.
24.3.3. Adding crosses
The sixth column of the GRINKOUT file contains a CHARACTER*1 variable IHET. This is normally a blank for ATOMS, or a star * for HETATMS. It is also a star * for hydrogen atoms whose positions have been computed by Programme GRIN, or a plus sign + for Special Records.
This variable may be changed to a cross X by editing GRINKOUT. The effect of the cross will be to cause the next Programme GRID to ignore the crossed atom. The explicit symbol to be used for the cross is a CAPITAL XLET: X.
Care must be taken not to cross an atom which donates a hydrogen-bond, without also crossing out its covalently bonded partner. For example, if the oxygen of a hydroxyl group is crossed out, it would also be necessary to cross out the covalently-bound hydroxyl hydrogen.
Care must also be taken about the last Target ATOM before the list of Target HETATMS. If this last ATOM (or the first HETATM) is crossed out, then the next Programme GRID will not know if the crossed-out record referred to an ATOM or to a HETATM. This distinction is normally shown by the presence of a blank character or a star, but such characters at the ATOM/HETATM change over point would be obliterated by your cross. In this case appropriate warnings will usually be printed to GRIDLONT by Programme GRID at run time.
Care must finally be taken to observe the effect of crossing out any atom, upon the overall electrostatic charge of the Target. It may be appropriate to edit the GRINKOUT file in order to modify the charges on nearby atoms.
The use of the cross allows the same GRINKOUT file to be used with or without certain atoms. Note however, that LINES MUST NEVER BE DELETED FROM A GRINKOUT FILE, AND MUST NEVER BE ADDED. THE SEQUENCE IN WHICH THE LINES ARE LISTED SHOULD NEVER BE ALTERED NOR SHOULD THE FIRST TWO NUMBERS AT THE START OF ANY LINE. Such changes would corrupt the connectivity matrix of the Target. However, the use of crosses provides the same effect without actually deleting lines.
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