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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