Insight II notes

InsightII 2000 is licensed for use on departmental SGI worksatations. Questions about the license should be directed to the MolViz Facility Staff.

Table of Contents

• Introduction
• Viewer notes
• Builder notes
• Discover (minimization) notes
• Simulated Annealing notes
• Simulated Annealing input files
• Docking notes
• Superimposing structures
• Forcefields
• Michael Seewald's notes about coloring residues according to a property that has been saved in a simple UNIX text file.
• PERL Scripts for InsightII
• Tutorials (for C687 Spring 1999)
  • Viewer
  • Builder/Biopolymer
  • Atomic & Molecular Properties
  • Energy Minimization
  • Molecular Dynamics
  • Docking
  • Surface Area Measurements, Ligand Design, etc.

These notes are a practical guide to general molecular modeling practices using InsightII. Refer to the InsightII manuals for a more complete description in order to tailor the molecular modeling to your specific applications. The hardcopy manuals for InsightII v95.0 and v96.0 are located in room A701. The InsightII 2000 manuals are available online at http://www.accelrys.com/doc/life/insight2K (contact the MolViz staff for user ID & password).

Format of these Documents

Menus and sub-menus are described as <main menu>/<sub-menu>. For instance molecule/get specifies the get sub-menu under the molecule main menu. All mouse-accessible selections are made by positioning the mouse cursor and clicking the LEFT mouse button. Keys that must be pressed simultaneously, or function keys, are listed in "<>" (e.g., <control-D> or <F9>).

1. Log on to pchem01-06, stereo1, stereo3, lexington, or splatter.
2. Open a UNIX window: Click on Tools/Shell
   Optional: If you don't have a Protein Data Bank (PDB) file, type
   cp /remote/sever/msi/I2000/tutorial/myoglobin.pdb $HOME. If you have a PDB file, make sure the file name has a .pdb extension, an is in your home directory.
3. Type insightII or insight2 to launch the program (version 2000.1)*. The program requires about a minute to generate windows and graphics.
4. To exit the program, type quit

*  Two previous versions of Insight II, 98 and 2000, are also available. To launch an old version, first type setup_biosym to initialize window, then type set_context 980 or set_context I2000 to set version, then type insightII or insight2 to launch the program.

Description of Licensed Modules

Viewer

allows user to display and manipulate molecules and other InsightII information. This module is active when InsightII is started, and it remains active during the entire session.

Builder

allows user to construct new molecules from molecular fragments or individual atoms. Allows user to modify type, hybridization, potential function parameters, bond order, and geometry of a molecule

Ampac/Mopac

interface to public-domain Ampac and Mopac programs for determination of molecular orbital shapes

Discover

energy minimization and dynamics.

Discover_3

assists the user in setting up complicated dynamics experiments.

Analysis

provides tools for evaluation of Discover calculations

Docking

calculates the non-bond energy between two molecules using exact atoms or using a precomputed energy grid. Assists the user in positioning the two molecules before submitting the molecular complex to Discover to minimization.