Appendix H. Table of keywords for programme GREAT

Programme GREAT is used in order to prepare and submit Programmes GRIN and GRID. It is controlled by the following Keywords. They are listed below with only the briefest of definitions. Keywords can normally be abbreviated to four characters. Those for which more characters are required in order to make them unique, are marked with a star *

 KEYWORDS FOR PREPARING PROGRAMME GRIN   (These Keywords are
 *************************************    not always active)

 ABANDON      Abandon what you are doing
 ALHY         Assign polarizability of (ATOM) hydrogen
 BACKWARDS    Change search direction for renaming atoms
 CARBON       Rename carbon atoms 
 CHANNEL      Input channel numbers 
 CLOSE        Close and save your edited PDB file 
 COORDINATES  Input name of PDB file of coordinates 
 DEFAULT      Input name of default directory 
 DISPLAY      Prepare the command file and then display it
 EFHY         Assign number of electrons in (ATOM) hydrogen 
 ELSE         Change to another main menu 
 FORWARDS     Change search direction for renaming atoms
 GRIN         Input name of executable Programme GRIN 
 GRINKOUT*    Input name of output file going to GRID 
 GRINLOUT*    Input name of lineprinter output file 
 GRUB         Input name of Datafile GRUB 
 HALOGENS     Rename halogen atoms
 HELP         Help
 HYDROGENS    Rename hydrogen atoms 
 IHVA         Switch on bulk properties of (ATOM) hydrogens 
 INAT         Channel number for input of GRUB datafile 
 INKO         Channel number for input of PDB file
 INSPECT      Inspect the command file for Programme GRIN 
 KOUT         Channel number for output file going to GRID
 LEVL         Controls amount of printing to lineprinter. 
 LOUT         Channel number for lineprinter output 
 NAME         Input name of command file (grin.in) 
 NITROGEN     Rename nitrogen atoms 
 ONLINE       Run Programme GRIN online 
 OXYGEN       Rename oxygen atoms 
 PASSWORD     Input password
 PHOS         Rename phosphorus atoms 
 PREPARE      Prepare command file for Programme GRIN 
 QQHY         Assign charge of (ATOM) hydrogen
 QUIT         Quit
 SPAWN        Spawn the operating system
 STOP         Stop what you are doing now 
 SUBMIT       Submit your job as a background job 
 SULPHUR      Rename sulphur atoms
 VDHY         Assign Van der Waals radius of (ATOM) hydrogen
 

 KEYWORDS FOR PREPARING PROGRAMME GRID   (These Keywords are
 *************************************    not always active)

 ABANDON      Abandon what you are doing
 ALPH         Set polarizabilty of single-atom Probe
 BOTX         Set bottom corner of GRID cage
 BOTY         Set bottom corner of GRID cage
 BOTZ         Set bottom corner of GRID cage
 CAGE         Set shape and size of GRID cage 
 CHANNEL      Input channel numbers 
 CHAR         Set charge of single-atom probe 
 CLEARENCE    Set clearence round Target
 COMMENT      Enter a comment line to grid.in
 CUBIC        Make a cubic GRID cage (x=y=z)
 DEEP         Controls amount of lineprinter output 
 DEFAULT      Input name of default directory 
 DISPLAY      Prepare the command file and then display it
 DPRO         Dielectric constant in middle of protein
 DWAT         Dielectric constant of environment
 EACH         Eliminate weak interactions from lineprinter tables
 ELSE         Change to another main menu 
 EMAX         Large positive cut-off energy 
 EMIN         Set hydrogen bond strength of single-atom Probe 
 FARH         Cut-off distance for hydrogen bonds 
 FARR         Cut-off distance for Lennard-Jones effects
 FILE         Choose a file of Energy Variables for Probe 
 GRID         Input name of executable Programme GRID 
 GRIDLONT*    Input name of lineprinter file
 GRIDKONT*    Input name of file with GRID energies 
 GRINKOUT*    Input name of GRINKOUT input file from GRIN 
 H-BOND       Set hydrogen-bond properties of Probe 
 HELP         Help
 INPT         Channel number for input of GRINKOUT file 
 INSPECT      Inspect the command file for Programme GRID 
 JTYPE        Set hydrogen bond "Type" of single-atom Probe 
 KONT         Channel number for file with GRID energies
 KWIK         Do a quicker computation
 LENG         Controls length of lineprinter tables 
 LEVL         Controls amount of printing to lineprinter. 
 LIST         Controls header of file of GRID energies
 LONT         Channel number for lineprinter output 
 LEAU         Switch for extra water computations 
 MENU         Displays menu of Probes listed by symbol
 NAME         Input name of command file (grid.in) 
 NEFF         Set number of electrons of single-atom Probe
 NETA         Number of hetatms to be included
 NPLA         Number of planes of grid points per Angstrom
 NUMB         Controls number of tables to lineprinter
 ONLINE       Run Programme GRID online 
 PARAMETERS   Set parameters describing single-atom Probe 
 POINT        Define position of one grid point 
 POSITION     Defines position of one grid point
 PREPARE      Prepare command file for Programme GRID 
 PROBE        Set properties of the Probe 
 PROGRAMME    Input name of executable Programme GRID 
 QUIT         Quit
 RMIN         Set hydrogen bond length for single-atom Probe
 SEVE         Choose several Probes from a Menu 
 SPAWN        Spawn the operating system
 STOP         Stop what you are doing now 
 SUBMIT       Submit your job as a background job 
 SURROUND     Grid cage will surround the whole Target
 TOPX         Set top corner of grid cage 
 TOPY         Set top corner of grid cage 
 TOPZ         Set top corner of grid cage 
 VDWR         Set Van der Waalks radius of single-atom Probe

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