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 

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