GRID manual

Table of Contents

I. Introduction to the GRID package

1. GRID22 - Changes from previous editions

1.1. The GLUE docking programme
1.2. The WINDOWS support has been started
1.3. Advanced MIF viewer
1.4. IHAC directive (controls the method for charge distribution)
1.5. The number of single-atom Grid probes has been increased from 56 to 64
1.6. New values for KWIK directive
1.7. New parameterisation for fluorine and heavier halogens
1.8. The GREATER interface has been upgraded
1.9. A pdf version of the manual is now available

2. GRID Installation

2.1. Installing GRID
2.2. Obtaining licenses for GRID
2.3. Customising the GRID environment.

3. General introduction

3.1. Overview of programme GREATER
3.2. Overview of programme GREAT
3.3. Overview of programme GRIN
3.4. Overview of programme GRID
3.5. Overview of programme GVIEW
3.6. Overview of programme GLUE
3.7. Overview of utility programmes

4. Programme GREAT

4.1. Format conversion by programme GREAT
4.2. Rapid format conversion by programme GREAT
4.3. Preparing a set of targets with GREAT

II. Programme GRIN

5. Introduction to programme GRIN

5.1. Abstract
5.2. Functions of programme GRIN

6. User guide to programme GRIN

6.1. Structure of programme GRIN
6.2. Input and output channels
6.3. Input to programme GRIN

7. Programme modes

7.1. Small molecule mode
7.2. Macromolecule mode
7.3. Mixed mode
7.4. Set mode

8. Extended Atoms

9. ATOMS and HETATMS in the same molecule

10. Protein Data Bank input

10.1. HEADER records
10.2. ATOM records
10.3. ATOM records for hydrogens
10.4. TER records
10.5. NAMIDE records
10.6. NTER records
10.7. HETATM records
10.8. Water records
10.9. END records
10.10. Inputting a set to Programme GRIN

11. Datafile GRUB

11.1. Atoms in datafile GRUB
11.2. Hetatms in datafile GRUB

12. Nomenclature of ATOMs and HETATMs

12.1. ATOMs in recognised molecules
12.2. ATOMs in unknown molecules
12.3. Hetero atoms in hetero molecules
12.4. HETATM names
12.5. ATOM/HETATM differences
12.6. ATOM and HETATM hydrogens

13. Energy variables

13.1. Atom variables in datafile GRUB
13.2. HETATM variables in datafile GRUB
13.3. Additional energy variables

14. Hydrogen bonds

14.1. Hydrogen bond geometry

15. Hydrogen bonds

15.1. Hydrogen bonding "types"

16. Computing the hydrophobic energies

16.1. The favourable components WENT and ELJ
16.2. Unfavourable hydrophobic components
16.3. Output tables for the hydrophobic probe
16.4. The hydrophobic probe with flexible targets
16.5. Hydrophobic summary

17. "Types" of metal cation

17.1. Metal cation probes
17.2. Metal cations of the target
17.3. Chloride counter-anions

18. Flexible target atoms

18.1. Types of flexible target atoms
18.2. Type specifications
18.3. Hydrogen case
18.4. Hydrogen bonds of multi-atom probes
18.5. Hydrogen bonds in unknown molecules
18.6. HETATM hydrogen bonds

19. Electrostatic charges in Target molecules

19.1. ATOM charges
19.2. HETATM charges

20. Directives for programme GRIN

20.1. Directives controlling input/output channels
20.2. Control directives

21. Output from programme GRIN

21.1. GRINLOUT files
21.2. GRINKOUT files
21.3. Hydrogen records in GRINKOUT
21.4. Conformationally flexible Targets

22. Messages from GRIN at run time

22.1. Severity of messages and warnings
22.2. List of messages and warnings from programme GRIN at run time
22.3. Other messages from GRIN

23. Parameter statements in programme GRIN

24. Editing Files

24.1. Editing datafile GRUB
24.2. Editing input file PDB
24.3. Editing output file GRINKOUT

III. Programme GRID

25. Introduction to programme GRID

25.1. Energy functions of programme GRID

26. User guide to programme GRID

26.1. Structure of programme GRID
26.2. Programme modes
26.3. Input and output channels
26.4. Input to programme GRID

27. Directives for programme GRID

27.1. Directive IEND
27.2. Other directives for GRID
27.3. Directives controlling input/output channels

28. Control directives

28.1. Observations at one grid point only
28.2. Timings with programme GRID
28.3. Control directives for GRID

29. Directives controlling the choice of the probe

29.1. Table of single-atom probes which can be called by their symbol
29.2. Table of multi-atom probes which can be called by their symbol

30. Comments

31. Input parameters

31.1. The job title for the Grid run
31.2. The Z-plane parameters
31.3. The energy variables for the probe
31.4. Table of JTYPE values for single-atom probes

32. Metal cation probes

33. Multi-atom probes

33.1. The aliphatic carboxylate probe COO-
33.2. The aromatic carboxylate probe AR.COO-
33.3. The aliphatic amide probe CONH2
33.4. The aromatic amide probe AR.CONH2
33.5. The aliphatic cis or trans amide probe CONHR
33.6. The aromatic cis or trans amide probe AR.CONHR
33.7. The aliphatic amidine probe AMIDINE
33.8. THe aromatic amidine probe AR.AMIDINE
33.9. The meta-diamino-benzene probe

34. Competition between probe and water

35. Output from programme GRID

35.1. GRIDLONT
35.2. Gridkont as a binary file
35.3. GRIDKONT with directive POSI

36. Studying a set of targets with Grid

36.1. Preparing a "file.list" for programme Grid
36.2. Using the "file.list" for programme Grin
36.3. Preparing a set of targets with programme Great
36.4. General procedure for inputting a set

37. Output from GRID for CoMFA

37.1. Studying the GRIDKONT file
37.2. Post-processing the GRIDKONT file
37.3. Post-processing GRIDKONT for CoMFA
37.4. Preparing a molecular database for CoMFA
37.5. Column nomenclature
37.6. GRID/CoMFA summary
37.7. Atom names for display on Sybyl

38. Output from GRID for GOLPE or SIMCA

39. Messages from GRID at run time

39.1. Severity of messages and warnings
39.2. List of messages and warnings from programme Grid at run time
39.3. Other messages from Grid

40. Techniques for using GRID

40.1. Checking ligand fit to a receptor
40.2. Organised water
40.3. The design of mutant proteins

IV. Programme GLUE

41. Programme GLUE

41.1. Introduction to programme GLUE
41.2. Overall method used by programme GLUE
41.3. User guide to programme GLUE
41.4. Running GLUE starting from FLAP sites
41.5. Using ligands as probe molecules in GLUE
41.6. General method to compute the binding energy for ligands as probe molecules in GLUE
41.7. List of energy terms
41.8. GLUE limitations

V. Support programmes

42. Programme names

43. Utility programmes

44. Alphabetical list of utility programmes

44.1. Programme A2K
44.2. Programme B2P
44.3. Programme FILMAP
44.4. Programme GCHEM
44.5. Programme GCNT
44.6. Programme GINS
44.7. Programme GKONT
44.8. Programme GMOL2 - GSDF
44.9. Programme GSIM
44.10. Programme G2F
44.11. Programme K2A
44.12. Programme A2K
44.13. Programme K2C
44.14. Programme K2F
44.15. Programme K2I
44.16. Programme K2M
44.17. Programme M2K
44.18. Programme K2S
44.19. Programme MINIM

VI. Graphical user interface (GUI)

45. Gview

45.1. Graphical representation of MIF
45.2. Drag and drop import
45.3. Mouse interaction
45.4. Gview status line
45.5. Gview menu

46. Greater

46.1. Installation and configuration
46.2. Importing target structures into Greater
46.3. Neutralise targets
46.4. Defining a GRID computation
46.5. Running a GRID computation
46.6. Using the results of a GRID computation
46.7. Saving and loading Greater computations
46.8. PDB filtering details

VII. Tutorials

47. List of tutorials

47.1. Greater tutorials
47.2. Great Tutorials
47.3. Glue Tutorials

48. Greater tutorial 01

48.1. Prediction of favourable locations of water molecules around a protein
48.2. WORKED EXAMPLES

49. Greater tutorial 02

49.1. HYDROPHOBIC Molecular Interaction Field

50. Greater tutorial 03

50.1. Greater with a list of proteins

51. Greater tutorial 04

51.1. A single small molecule example

52. Greater tutorial 05

52.1. Macromolecular hydration and neutralisation

53. Greater tutorial 06

53.1. Detecting Competition between a Ligand and Water

54. Greater tutorial 07

54.1. MIFs for a set of passively absorbed drugs.

55. Tutorial 01

55.1. How to start
55.2. WORKED EXAMPLES

56. Tutorial 02

56.1. HYDROPHOBIC Molecular Interaction Field

57. Tutorial 03

57.1. ANOTHER WORKED EXAMPLE

58. Tutorial 04

58.1. A MORPHINE EXAMPLE

59. Tutorial 05

59.1. MIFs for a set of passively absorbed drugs.

60. Tutorial 06

60.1. Detecting Competition between a Ligand and Water

61. GLUE Tutorial 01

61.1. Docking a ligand into a Target protein

62. GLUE Tutorial 02

62.1. Docking a Ligand into a Target Protein.
62.2. Protein input structure
62.3. Site points preparation
62.4. Site points visualization and selection
62.5. Ligand preparation
62.6. Automatic docking

VIII. Appendix and Figures

A. Mnemonics and symbols

B. Table of types of target ATOMS/HETATMS

C. Table of probe types

D. GRUB table of recognized molecules

E. GRUB table of HETATM symbols

F. Table of probe names

G. Table of multi-atom probes

H. Table of keywords for programme GREAT

I. Table of atom names for group probes

J. File types and file-changing programmes

K. Figures

K.1. Example of a PDB file
K.2. Relationship between Programmes, Directives, Files and Channels
K.3. The lineprinter output file GRINLOUT
K.4. The first part of an input file GRUB
K.5. The first part of a GRINKOUT file
K.6. Sample of directives and parameters for Grid
K.7. Initial part of the GRIDLONT output
K.8. Output table of the GRIDLONT output

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GRID manual

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