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Chapter 47. List of tutorials
Starting from version 20 of the GRID package, a new program called Greater is distributed along with the usual programmes; this is basically a graphical front-end that can help the user dealing with the different tasks involved in the GRID use. Therefore all the tutorials pages has been updated to use Greater as the default interface. The User may select the new tutorial explicitly designed for Version 22, or the tutorials for the older version of Grid. We suggest all Users should try the new tutorials made using the Greater graphical front end. However, not all the Great functions and capability are currently introduced inside Greater. Please read the manual for specific use of Great directives and options.
For further information or questions regarding these tutorials, the user manual or the programmes, feel free to contact us using our web site http://www.moldiscovery.com
47.1. Greater tutorials
Several detailed tutorials, updated to use GREATER as default interface, are supplied with this version of GRID:
- Greater Tutorial 01
It is the basic Tutorial for GREATER. Explains how to use programmes GRIN and GRID under the control of supervising graphic program GREATER. Explains how to use Gview to visualise the produced Molecular Interaction Field.
- Greater Tutorial 02
Explains how to obtain other Molecular Interaction Fields. Explains how to visualise the produced GRIDKONT data file.
- Greater Tutorial 03
Explains how to use program GREATER to convert a list of PDB target proteins in a single run., using the new PDB automatic filtering.
- Greater Tutorial 04
It is an example of conversion from Sybyl mol2 Format to GRID format supervised by GREATER, followed by a Molecular Interaction Field calculation.
- Greater Tutorial 05
Demonstrates the performance of the program GREATER for the transformation of mol2 format in GRID-pdb format when working in set of small molecules.
- Greater Tutorial 06
It is an application of the program GREATER and GRID in Reverse Mode for detection of disfavoured places in receptor clefts.
- Greater Tutorial 07
Demonstrates how to hydrate and neutralise macromolecular structures in automatic way.
47.2. Great Tutorials
The old Tutorials based on the GREAT programme are still present in this distribution. Tutorials from 01 to 04 are intended for first time Users since they show the basic operations necessary to accomplish the most common tasks in GRID daily use. Tutorials 05 and 06 are intended for Experienced Users or by Users whenever they have acquired the notions contained in the first four tutorials. More working examples are inserted inside the MD User manual. Here it is the list of the tutorials for the previous version of the programmes (oldl Tutorials are still fully functional):
- Tutorial 01 - no graphic interface
Explains how to use programmes GRIN and GRID under the control of supervising program GREAT. Explains how to visualise the Molecular Interaction Field produced by GRID with program GVIEW.
- Tutorial 02 - no graphic interface
Explains how to change the GRID command file in a quick way to obtain others Molecular Interaction Fields. Explains how to visualise the produced GRIDKONT data file.
- Tutorial 03 - no graphic interface
Explains how to use program GREAT with ATOM or HETATM (macro)molecular structures.
- Tutorial 04 - no graphic interface
It is an example of conversion from Cambridge Data Bank Format to PDB format followed by a Molecular Interaction Field calculation
- Tutorial 05 - no graphic interface
Demonstrates the performance of the program GMOL2 for the transformation of mol2 format in GRID-pdb format when working in set of molecules.
- Tutorial 06 - no graphic interface
It is an application of the program GRID in Reverse Mode for detection of disfavoured places in receptor clefts.
47.3. Glue Tutorials
- Tutorial Glue 01
Explains how to proceed with a simple docking project.
- Tutorial Glue 02
Explains how to proceed with a more complex docking project.
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