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Chapter 43. Utility programmes
Several utility Programmes are provided in order to support the four main Programmes GRIN, GRID, GLUE and GREAT. These utilities are listed here in alphabetical order:
- PROGRAMME A2K.
Converts an ASCII eye-readable copy of a standard GRIDKONT file, back into the original binary code (see K2A).
- PROGRAMME B2P.
Converts the binary output file which is produced by Programme Grid when directive POSI has been set, into eye-readable PDB format. It similarly converts the binary output files from Programmes FILMAP and MINIM.
- PROGRAMME FILMAP.
This is used in conjunction with Programme MINIM, in order to populate a Grid map in the energetically most favourable way; e.g. to hydrate a protein, or provide it with appropriate counter-ions.
- PROGRAMME GCHEM.
When several Targets have been studied together as a Set, using a FILE.LIST, this Programme converts the output from GRID into a Set of .CHE files which can be used as input to the Chem-X graphics software of Oxford Molecular.
NOTE You must set Directive LEVL>0 if you are doing a Grid run, and want to postprocess the output through GCHEM.
- PROGRAMME GCNT.
When several Targets have been studied together as a Set, using a FILE.LIST, this Programme converts the output from GRID into a Set of .CNT files which can be used as input to the CoMFA package of TRIPOS Associates Inc.
- PROGRAMME GINS.
When several Targets have been studied together as a Set, using a FILE.LIST, this Programme converts the output from GRID into a Set of .GRD files which can be used as input to the INSIGHT graphics software of MSI.
NOTE You must set Directive LEVL>0 if you are doing a Grid run, and want to postprocess the output through GINS.
- PROGRAMME GKONT.
When several Targets have been studied together as a Set, using a FILE.LIST, this Programme converts the output from GRID into a Set of standard GRIDKONT files each having one Grid map for one Probe on one Target molecule.
NOTE You must set Directive LEVL>0 if you are doing a Grid run, and want to postprocess the output through GKONT.
- PROGRAMME GMOL2
Converts the sybyl mol2 molecular structures into PDB format.
- PROGRAMME GSIM.
When several Targets have been studied together as a Set, using a FILE.LIST, this Programme converts the output from GRID into a format which can be used as input to the SIMCA package of UMETRI.
- PROGRAMME GSDF
Converts a sdf file of molecular structures into several PDB format files.
- PROGRAMME G2F.
Alters the names in a GREAT.LIST file, stripping the extensions (eg: .PDB or .CSSR) from each name to leave a FILE.LIST of base names.
- PROGRAMME K2A.
Converts a standard binary GRIDKONT file into an ASCII eye-readable copy (See A2K above).
- PROGRAMME K2C.
Converts a standard binary GRIDKONT file into the format required for input to the Chem-X graphics software of Oxford Molecular.
- PROGRAMME K2E.
Converts a standard binary GRIDKONT file into the format required for input to Iris Explorer.
- PROGRAMME K2F.
Converts a standard binary GRIDKONT file into another ASCII format which can be used as input to some graphics software(e.g. FRODO).
- PROGRAMME K2I.
Converts a standard binary GRIDKONT file into the format required for input to the INSIGHT graphics software of Molecular Simulations. Inc.
- PROGRAMME K2M.
Converts a standard binary GRIDKONT file into the .MINI format required for input to Programme GLUE.
- PROGRAMME K2S.
Converts a standard binary GRIDKONT file into the format required for input to the SYBYL graphics software of TRIPOS Associates Inc.
- PROGRAMME MINIM.
Finds all the energy minima in a standard binary GRIDKONT file.
- PROGRAMME M2K.
Converts the .MINI format used as input by Programme GLUE into a standard binary GRIDKONT file.
These utility Programmes may be divided into six subgroups:
Programmes A2K, K2A, K2C, K2E, K2F, K2I, K2M, K2S, M2K and MINIM which are used in order to deal with the standard version of GRIDKONT . These Programmes are described in detail below, and may be run directly from the keyboard. For example, to run k2a on a Unix-style system one types: k2a in answer to the Unix prompt. Programme A2K is normally used after K2A, and is therefore described immediately after it (see below). Similarly, M2K is described after K2M. The other Programmes are listed alphabetically.
Programme B2P is used in order to deal with a special GRIDKONT format which is output when the positions of the individual grid points are defined by POSI records. This Programme B2P is run directly from the keyboard, and prepares an eye-readable PDB file from the non-standard binary GRIDKONT file which is produced when directive POSI has been set. It similarly converts the binary output files produced by Programmes FILMAP and MINIM.
Programmes GCHEM, GCNT, GINS, GKONT and GSIM deal with the special output which is written by GRID when a number of Targets have been studied together as a Set. These Programmes are described in detail above, under the heading STUDYING A SET OF TARGETS WITH GRID.
Note: You must set Directive LEVL>0 if you are doing a Grid run, and want to postprocess the output through GCHEM or GINS or GKONT.
Programme G2F is used to change a GREAT.LIST file into a FILE.LIST. It is described above under the heading PREPARING GREAT.LIST.
Programme FILMAP takes the list of energy minima produced by MINIM, and populates these minima in the energetically most favourable way
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