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Chapter 35. Output from programme GRID
Output consists of two components: the lineprinter file GRIDLONT and the computer readable binary file GRIDKONT.
Alternatively the GRIDKONT output can be obtained as User-Readable ASCII characters.
35.1. GRIDLONT
GRIDLONT is the lineprinter output file. It begins with a list of directives and other details for checking purposes, and then gives the results of the calculation. Part of a sample GRIDLONT file is shown in Section K.7 and Section K.8. The layout and amount of information is controlled by directives DEEP, LENG, LEVL and NUMB as described above.
Each line written in the GRIDLONT relates to the interaction between the Probe and one particular atom of the Target molecule. Many of these variables have been defined above under Programme GRIN. The new variable names are:
- DISTLJ (real)
is the optimum distance (as calculated on the basis of the Lennard-Jones function alone) between the Probe and the Target atom on this particular line of output file GRIDLONT.
- DIST (real)
is the actual distance between Target atom and Probe.
- DISTHB (real)
is the optimum distance calculated on the basis of the hydrogen-bonding function alone.
- QATOM (real)
is the charge on the Target atom, i.e. Q(I).
- EQ (real)
is the energy contribution made by the electro-static interaction between the Target atom and the Probe.
- ELJ (real)
is the energy contribution made by the Lennard-Jones component of the interaction. All energies are in Kcal/mole.
- EH (real)
is the energy contribution made by the hydrogen bond component of the interaction.
- DA
is a CHARACTER*1 variable which is the character D if the Probe donates its hydrogen bond to the Target atom, or the character A if the Probe is accepting a hydrogen bond from the Target. This distinction may not be obvious when, for example, a water Probe interacts with a hydroxy group of the Target. In some cases there is a very fine energetic balance between a donated and an accepted hydrogen bond. Variable DA will then show what Programme GRID actually did, but the alternative choice might well be equally valid.
- ET (real)
is the total energy of interaction calculated between the Target atom and the Probe, i.e: ET = ELJ+EH+EQ
- EFD (real)
is the effective dielectric constant used to calculate the pairwise electrostatic interaction between the Target atom and the Probe.
The number -99.99 sometimes appears as the value of ELJ or EH. This dummy value is used because it is outside the range of feasible values.
When ELJ = -99.99 in GRINLOUT the Probe is close to the Target atom, and there is a hydrogen bonding attraction (i.e. EHB is negative) but a Lennard-Jones repulsion has been computed (ELJ positive). In these circumstances the Lennard-Jones repulsion is suppressed and -99.99 is printed to GRIDLONT. However this dummy value is not carried forward to the row or column totals, and is not added to the GRID value in the computer-readable output file GRIDKONT. ELJ is simply ignored under these special circumstances, in which there is a mutual hydrogen-bonding attraction between the atoms.
When EH= -99.99 there may be more hydrogen-bonding atoms on the Target than the number of hydrogen bonds which can be made by the Probe. In these circumstances some of the Target atoms will make hydrogen bonds, and others will be rejected. The dummy value -99.99 may indicate a hydrogen-bonding atom of the Target which has been rejected in this way, or may show that the configurational relationship between Target and Probe atoms does not permit effective hydrogen bonding. Note that the dummy value -99.99 is not carried forward to the row or column totals in GRIDLONT, and is not added to the GRID value in the computer-readable output file GRIDKONT.
35.1.1. Other interactions
Some of the interactions of the hydrophobic Probe cannot be described as atom-atom effects between the Probe itself and one explicit Target atom. These include the entropic component associated with ordered water in the hydration shell, and its modification by polar interactions between water and hydrogen-bonding Target atoms. The tables in a GRIDLONT file may therefore have an extra line which shows ADJUSTMENTS FOR ENTROPY AND FOR OTHER INTERACTIONS. This extra line is only displayed when the hydrophobic or amphipathic Probe is being used.
35.1.2. Entropy of flexible sidechains
Movements of flexible side-chains of the Target will be taken into account when directive MOVE>0, and an entropic term therefore enters into the computations. This cannot always be incorporated into an individual Atom-Probe energy term, and so an overall adjustment may sometimes be made for the entropy of flexible side-chains.
35.1.3. Close contacts by the multi-atom probe
It is not easy to tabulate all the contacts made by all the atoms in a multi-atom Probe. Most interactions will be favourable at an energy minimum, but some of the Probe atoms may make unfavourably close contacts. The tables in a GRIDLONT file may therefore have an extra line which shows the ADJUSTMENT FOR CLOSE CONTACTS BY 'OTHER' ATOMS OF THE MULTI-ATOM PROBE.
35.2. Gridkont as a binary file
GRIDKONT is the computer readable binary output file. It may be used for further computations, or for graphical display. An effective method is to study the interaction energy of a Probe as a three-dimensional contour surface, together with the structure of the Target molecule. Difference maps can also be calculated between the computed energies for two different Probes, and may be used to detect regions where the Target molecule shows a preference for one Probe rather than the other.
File GRIDKONT is not written if a single grid point is specified by making TOPX=BOTX and TOPY=BOTY and TOPZ=BOTZ as described above.
35.3. GRIDKONT with directive POSI
Programme GRID can calculate the interactions of the Probe at a series of predefined grid points. The x,y,z coordinates of each point are set with directive POSI. Upto 100000 POSI values may be defined.
When one Probe is studied at several positions defined by POSI, the binary GRIDKONT output file contains a single record for each POSItion. This record contains the unformatted binary values of x, y, z and E for the POSItion, and the GRIDKONT file may then be used as input for further computations.
For certain applications, such as the computation of GRID maps for the comparison of compounds, the User might want to write a jiffy program which prepared an appropriate list of POSI values. This list can be pasted to the grid.in command file. Any distribution of grid points can be achieved. For example, one might want grid points distributed at spherically or cylindrically defined positions, or on the surface of a molecule, instead of points on an orthogonal Grid. It should be noted, however, that the graphic programme Gview may not be able to display the results unless the Grid map is conventionally arranged. You may therefore have to make your own arrangements for analysing the results.
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