Appendix A. Mnemonics and symbols
Most variable names in the Programmes have mnemonic
derivations. They are listed here as an aide memoire, together with
other symbols which are used.
A Suffix for variables relating to Atoms
A Suffix for variables relating to hydrogen bond Acceptors
A2K Programme converting Ascii to gridKont format
ACID AminoACID
ALHY ALpha (polarizability) of H-bonding hYdrogen atoms
ALMD ALMD is a directive reporting the Target atom which interacts most
strongly at each grid point.
ALPHA Alpha is a common symbol for polarizability
ALT Descriptor showing an ALTernative position for an atom
ATM AToM
BOTX BOTtom value of X
BVAL Thermal parameter (B VALue). Also
used for closest approach of a moveable atom to its linker
CDB Cambridge Data Bank
CLER CLEaRance round the macromolecule
D Suffix relating to hydrogen bond Donors
DEEP Acceptable DEPth of energy minimum in GRIDLONT
DIST DISTance
DPRO Dielectric of the PROtein
DWAT Dielectric of WATer
E Potential Energy
EACH Check EACH atom for weak interactions
EFD EFective Dielectric constant
EL ELectrostatic
EMAX Energy MAXimum
EMIN The Energy at the MINimum of the h-bond function
FARR How FAR the lennaRd-jones potential will be computed
FARH How FAR the Hydrogen bond potential will be computed
FILMAP Programme for populating the minima in a grid MAP
GCNT Programme converting Gridkont files to Sybyl .CNT format
GMOL2 Programme to convert mol2 file in grid-pdb format
GREAT A GREAT supervising environment for the MD Programmes
GRID Programme dealing with a GRID of points
GRIDC File of GRID Subroutines for output to Chem-X
GRIDF File of GRID Subroutines which outputs standard Files
GRIDI File of GRID Subroutines for output to INSIGHT
GRIDP File of GRID Subroutines for output to GRASP
GRIDQ File of GRID Subroutines for output to QUANTA
GRIDS File of GRID Subroutines for output to SYBYL
GRIDKONT Programme GRID output for KONTours
GRIN Programme GRid INput
GRINKOUT Programme GRIN Koordinate OUTput
GRINLOUT Programme GRIN lineprinter OUTput
GSDF Programme to convert sdf file into grid-pdb file
GSIM Programme converting Gridkont files to SIMca format
GVIEW Programme to display grid map and molecules in 3D
H Suffix for variables relating to Hetatms
HB Hydrogen Bond
HEAD HEADer
HETATM HETero AToM
HYD HYDrogen
I Suffix for variables relating to the Target atoms
IA Index for hydrogen bond Acceptor
IDIR Channel for Input of DIRectives
IEND Index for the END of directive input
IHVA If H-bonding hydrogens are assigned energy VAriables
IN Suffix for INput values from datafile GRUB
INAT Channel for INput of ATom variables from datafile GRUB
INKO Channel for INput of KOordinates from file PDB
INPT Channel for INPuT of data from Programme GRIN
INSERT Descriptor for an INSERTion
ISUB Descriptor for Identifier for SUBunit
J Suffix for variables relating to the Probe
JTYPE Integer defining the hydrogen-bonding TYPE of an atom
K2A Programme converting gridKont file to Ascii format
K2C Programme converting Gridkont files to Chem-X format
K2E Programme converting Gridkont files for Iris Explorer
K2F Programme converting Gridkont files to a Frodo format
K2I Programme converting Gridkont files to INSIGHT format
K2M Programme converting Gridkont files into .MINI files
K2S Programme converting Gridkont files to SYBYL .CNT format
KONT Channel for output for KONTours
KOUT Channel for Koordinate OUTput
KWIK Makes the computation quicker
LENG LENGth of the tables
LEVL LEVeL of output information provided
LGND Channel for the Energy Variables which describe the LIGanD
LIST Controls the LIST of extra variables printed to GRIDKONT
LJ Lennard-Jones
LONT Channel for Lineprinter Output of Nearby Target atoms from Programme GRID
LOUT Channel for Lineprinter OUTput from Programme GRIN
LPIN Licenced Personal Identification Number
MARKER MARKs an atom which has an associated special record
MINIM Programme for finding energy MINIMa in a grid map
MOVE Controls MOVEment of torsion angles in the target
NAMIDE Nitrogen AMIDE linkage in protein backbone
NEFF The EFFective Number of electrons
NEHY EFfective Number of electrons of H-bonding hYdrogen
NETA Number of Extra Target Atoms
NPDB Number of the atom in the original PDB file
NPLA Number of PLanes per Angstrom
NRES Number of the amino-acid RESidue in the sequence. Also
used for numbering parts of the core and beads
NTER Nitrogen TERminal of the sequence
NUMB NUMBer
OCCUP OCCUPancy. Also used for the greatest distance of a
moveable target atom from its linker
OXT Extra OXygen atom at the carboxy Terminal of the sequence
PDB Protein Data Bank
POSI POSItion of required grid point
RMIN Radius corresponding to the MINimum of the h-bond function
Q A common symbol for electric charge
QQHY Charge (Q) of HYdrogen-bonding hydrogens bonded to ATOMS
SET Several Targets which are studied together as a SET
TER TERminal of sequence
TOPX TOP value of X |