44.1. Programme A2K

Programme A2K is described below after Programme k2a, since the Programmes are complementary. Similarly, m2k is described after k2m.

44.2. Programme B2P

When directive POSI has been used in order to define explicit grid points, the GRIDKONT output is a computer-readable binary file. Similar binary files may be output from Programmes FILMAP and MINIM. The binary files are concise and require little disk space, but they are not regular GRIDKONT files. Programme B2P may be used to translate them into standard eye-readable PDB format.

Programme B2P can be straightforwardly run from the keyboard. For example, the would be:

  b2p 
  TYPE THE NAME OF YOUR BINARY INPUT FILE: 
  gridkont.bin
  TYPE THE NAME OF THE FILE FOR THE PDB OUTPUT: 
  readable.pdb

The prompts from B2P are shown in CAPITAL letters in the above example, and the User's responses are in small type. You have prepared a new PDB file called: readable.pdb from the binary file: gridkont.bin which was originally output from Programme GRID using directive POSI. The output format for each POSItion in the new eye-readable PDB file is defined by the Write and Format Statements:

     WRITE (LOUT,1400) 
    +I,ATOM,ALT,ACID,ISUB,NRES,INSERT,X,Y,Z,ENERGY 
1400 FORMAT ('HETATM',I5,A5,A1,A4,A1,I4,A1,3X,3F8.3,F6.2)

from which it can be seen that the Grid energy at each POSItion is recorded in the column which is normally used for occupancy in PDB format. The molecule name will be MOL and each successive record will have a new molecule number starting with -999 -998 -997 and so on. Further information is given in Section 28.3.22.2.

The output from Programmes FILMAP and MINIM (see below) may also be produced as a binary file. Programme B2P can translate the binary output from FILMAP and MINIM into PDB files as just described. There is also an option in FILMAP and MINIM to produce PDB output directly if this is required. The binary output is shorter, but cannot be read by eye.

44.3. Programme FILMAP

Programme FILMAP is used in order to populate the energy minima in a Grid map. These minima must have been found previously by using Programme MINIM which is described below. We suggest that you read the description of MINIM before reading this description of FILMAP.

In the following example for FILMAP we are assuming that a water Probe has been used to generate a standard Grid Map called 'oh2.kont', and that Programme MINIM has already extracted the energy minima from that map into a file called 'oh2.minima'.

A ready-to-run executable copy of FILMAP is supplied on the CD-ROM. For example, the dialogue on a Unix system would be:

   filmap 
   ENTER FILENAME FROM WHICH TO READ THE XYZ-MINIMA: 
   oh2.minima 
   TYPE THE NAME OF THE FILE IN WHICH 
   THE SELECTED MINIMA WILL BE LISTED: 
   oh2.pdb 
   THE FINAL OUTPUT FILE CAN BE WRITTEN IN COMPUTER-READABLE 
   BINARY OR IN EYE-READABLE PDB FORMAT.       DO    YOU WANT 
   BINARY OUTPUT?   ANSWER YES OR NO OR HELP.   ANSWER NOW:    
   no

The prompts from FILMAP are shown in CAPITAL letters in the above example, and the User's responses are in small type. We normally recommend that you do not select binary output.

Programme FILMAP now presents you with a menu of Probes from which you would select OH2 for this example run. It then presents you with another menu which allows you to adjust several important parameters. These control the way in which the Programme works, which is by annealing successive Probes into the list of minima. In the case of water the Programme will allow the individual water Probes to hydrogen bond to each other whenever they find neighbouring minima at an appropriate distance from each other. Thus, if one water finds an energy minimum at Site A and another finds Site B, and if the A-B distance is about 2.8 Angstrom, there will be a tendancy for both these sites to be populated so that a favourable hydrogen-bond can be formed between the waters.

A different situation would apply if the initial grid Map had been generated by a potassium Probe. In this case the presence of a potassium at one site would tend to repel a second potassium from any nearby sites, and so Programme FILMAP would tend to distribute the potassiums well away from each other. This potassium behaviour would therefore be different to the behaviour with water, which tends to form hydrogen-bonding water clusters as the map is populated.

The menu allows you to alter the annealing schedule, but we suggest that you start by using the default values. Therefore choose 6 in the annealing menu, and the Programme will start to run as soon as you hit RETURN.

As Programme FILMAP runs it will report progress to the VDU, and you will see the energy of the system diminish. Eventually, after a number of cycles, no more successful moves can be made, and a list of the occupied minima is displayed. These are numbered according to the row numbers of the original input file (oh2.minima in our example), and you may have to hit RETURN if the list is too long for display on one VDU screen.

An output file (called oh2.pdb in our example because it is written in PDB format) is also prepared. It lists the populated minima in the calculated sequence of their binding energies which are shown in the last column of the file. The first line is the minimum at which water binds with the most favourable energy, and the energies tend upwards towards zero on subsequent lines. The coordinates of each position are given, and with a little editing one can append this Brookhaven .PDB file to the end of the original PDB file which was used to generate the initial Grid Map. In our example this would have the effect of partly hydrating the protein.

44.4. Programme GCHEM

Programme GCHEM is described in Chapter 36.

44.5. Programme GCNT

Programme GCNT is described in Chapter 36.

44.6. Programme GINS

Programme GINS is described in Chapter 36.

44.7. Programme GKONT

Programme GKONT is described in Chapter 36.

44.8. Programme GMOL2 - GSDF

One of the most time consuming steps, when applying GRID on small molecules, is to assign appropriate GRID atom types. From the version 19 two new tools are provided, that allow you to assign automatically atom types in a fast way and with a very high degree of accuracy: gmol2 and gsdf.

Gmol2 and gsdf convert molecular structures of small compounds from standard formats (TRIPOS mol2 and MDL sdFiles) into a PDB file in which the atom name contains appropriate atom types for GRID. The ouput file is suitable for being used directly as input for program GRIN.

The atom type assignment is made according to rules based on the molecular structure, geometry and connectivity. In the case of the mol2 files, no use is made of the SYBYL potential. On the contrary, the method assumes that the bond order of every bond in the molecule is correct or at least corresponds with a possible resonating structure. In some cases, the method uses also the 3D geometry of the molecule (for example, it checks the planarity of the ring to make sure of its aromaticity) and therefore the geometry of the input structures should roughly correspond with a reasonable low energy conformer.

Gmol2 and gsdf programs are non-interactive, because they have been designed for being integrated in scripts or automatic procedures. The conversion is rather fast and allows processing extremely large series of compounds in a short time.

44.9. Programme GSIM

Programme Gsim is described above under the heading Section 37.2.

44.10. Programme G2F

Programme G2F is used in order to change a GREAT.LIST file into a FILE.LIST. Both of these are lists of file names, but the extensions such as .PDB are not shown in the FILE.LIST.

Programme G2F strips off the extensions from the filenames in a list. It also strips off any subsequent characters, and the output is a single-column list of base filenames. Programme G2F is described in Section 4.3.1.

44.11. Programme K2A

Programme k2a is used in order to alter the format of a standard binary GRIDKONT output file from Programme GRID, into ASCII characters which can be read by the User. The explicit individual energy values at each grid point can then be studied in detail (although the ASCII output file from a whole protein may be very big. The name K2A is derived from "gridKont 2 Ascii" which means going from "gridkont to ascii".

44.12. Programme A2K

Programme A2K is used in order to retranslate the ASCII output from K2A back into the format of a standard binary GRIDKONT output file as written by the standard versions of Subroutines DRITE1 and DRITE2 in Programme GRID. The name A2K is derived from: "Ascii 2 gridKont" which means going from "ascii to gridkont".

For example, the dialogue on a system would be:

k2a

TYPE THE NAME OF YOUR ASCII FILE:

gridkont.asc

TYPE NAME FOR YOUR BINARY GRIDKONT OUTPUT FILE:

newgridkont.dat

The prompts from A2K are shown in CAPITAL letters in the above example, and the User's responses are in small type. 'FINISHED' is the final message showing that the job has been successfully completed. The User has prepared a new binary file called:

 newgridkont.dat

and may have done this on another computer after transmitting the ASCII file over a network. Note that newgridkont.dat will not be exactly the same as the original binary file gridkont.dat because some energy values will have been rounded in the translated ASCII file.

Problems may arise if the ASCII file has been edited by the User, and a warning may then be printed before Programme A2K stops.

44.13. Programme K2C

Programme K2C is used in order to alter the format of a standard GRIDKONT output file from Programme GRID, into the appropriate input format for the Chem-X graphics display software system. More information about Chem-X is available from Oxford Molecular Limited whose address is given above.

Programme K2C may be straightforwardly run from the keyboard.

   k2c 
   TYPE NAME OF YOUR GRIDKONT FILE: 
   gridkont.dat 
   TYPE NAME OF GRID MAP FILE FOR CHEM-X: 
   output.map

The prompts from K2C are shown in CAPITAL letters in the above example, and the User's responses are in small type. 'FINISHED' is the final message showing that the job has been successfully completed. The User has prepared a new file called: output.map ready for input to Chem-X, from the standard file: gridkont.dat which was originally output from Programme GRID.

44.14. Programme K2F

Programme K2F is used in order to alter the format of a standard binary GRIDKONT output file from Programme GRID, into ASCII characters which can be read by the User. It therefore resembles Programme K2A above, but the output format can be used in order to prepare a DSN6 map for some versions of FRODO and O.

Version 12 of Programme K2F was issued in January 1995, and caused the sign of the energies to be reversed in the ASCII output. This anomaly was amended in the next Version, and a negative sign is now given to a negative (ie: a favourable) energy. Therefore Versions 12 of K2F should no longer be used.

44.15. Programme K2I

Programme K2I is used in order to alter the format of a standard GRIDKONT output file from Programme GRID, into the appropriate input format for the INSIGHT graphics display software system. More information about INSIGHT is available from Molecular Simulations whose address is given above.

Programme K2I may be straightforwardly run from the keyboard. For example, the dialogue would be:

   k2i 
   TYPE NAME OF YOUR GRIDKONT FILE: 
   gridkont.dat 
   TYPE NAME OF GRID MAP FILE FOR INSIGHT: 
   gridkont.grd

The prompts from K2I are shown in CAPITAL letters in the above example, and the User's responses are in small type. The method for displaying the GRID contours on INSIGHT is described above (see contents under Display on INSIGHT).

44.16. Programme K2M

Programme K2M is used in order to change a standard GRIDKONT binary file into a shorter .MINI binary file which can be used as input for Programme GLUE. It is described above under the subheading PROGRAMME K2M in the Section for Programme GLUE in this User Manual.

44.17. Programme M2K

Programme M2K is used in order to change a .MINI binary file into a standard GRIDKONT binary file. (The .MINI files are used as input for Programme GLUE).

44.18. Programme K2S

Programme K2S is used in order to alter the format of a standard GRIDKONT output file from Programme GRID, into the appropriate input format for the SYBYL graphics display software system. More information about SYBYL is available from Tripos Associates Inc whose address is given above.

Programme K2S may be straightforwardly run from the keyboard. For example, the would be:

   k2s 
   TYPE NAME OF YOUR GRIDKONT FILE: 
   gridkont.dat 
   TYPE NAME OF GRID MAP FILE FOR SYBYL: 
   gridkont.cnt

The prompts from K2S are shown in CAPITAL letters in the above example, and the User's responses are in small type. The User has prepared a new file called: gridkont.cnt ready for input to SYBYL, from the standard file: gridkont.dat originally output from Programme GRID.

The method for displaying the GRID contours on SYBYL is described above (see contents under Display on SYBYL).

44.19. Programme MINIM

Programme MINIM is used in order to find the energy minima in a Grid map. It can be straightforwardly run directly from the keyboard. For example, the dialogue would be:

   minim 
   TYPE THE NAME OF YOUR GRIDKONT FILE: 
   gridkont.dat
   TYPE THE NAME OF THE OUTPUT FILE WITH THE MINIMA: 
   gridkont.min
   TYPE THE ENERGY THRESHOLD: 
   -8 
   DO YOU WANT INTERPOLATION: 
   no 
   DO YOU WANT BINARY OUTPUT: 
   no

The prompts from MINIM are shown in CAPITAL letters in the above example, and the User's responses are in small type. The Programme starts searching for minima as soon as the last question has been answered.

A minimum is defined in Programme MINIM, as a grid point which is completely surrounded by points at which the Grid energy is greater (more positive). Each minimum will be at the centre of a block of 3x3x3 grid points, making 27 points in the whole block. The neighbouring 26 points will have greater energies than the central point at the minimum. Note, therefore, that a minimum cannot lie on the outside surface of the Grid, because an outside point would not have 26 neighbours.

The above definition of a minimum does not specify its absolute energy value. Some "minima" could actually have positive energies, because they were surrounded by a cluster of points with even more positive energies. The threshold energy in the above example is therefore used in order to select the most appropriate minima in the Grid map. In this case the Programme will only choose minima which have a more negative energy than -8 Kcal/mole.

The real position of lowest energy round the Target will almost always lie somewhere between the observed grid points. It will only be at an actual Grid position by some fluke of chance. Programme MINIM therefore provides an interpolation facility, which can be used to estimate the actual position of lowest energy.

This interpolation will be most reliable when the Grid map is smooth, but the real energy profile round a Target can change quite quickly from place to place. Near the Van der Waals surface, for example, the energy alters abruptly from a positive to a negative value in less than half an Angstrom. We therefore do not recommend interpolation unless the grid points are closer than 0.25 Angstrom (Directive NPLA > 4).

The final output from Programme MINIM will be a list of energy minima, sorted with the most negative minima at the head of the list. The output can be in computer-readable binary or eye-readable PDB Format. A binary output file from MINIM can be changed into PDB by Programme B2P (See above). The binary output from MINIM is written by:

 WRITE (MINM) X,Y,Z,ENERGY

and the alternative PDB output is prepared by the Write and Format Statements described above under Programme B2P.

Programme MINIM will report progress while it is running. In the above example you will prepare a new PDB file called: gridkont.min from a regular GRIDKONT file: gridkont.dat.