CCMM Download Tutorials

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Adobe ACROBAT Reader or Plug-in from Adobe you can download it from adobe ACROBAT 

 

Several tutorials have been prepared to help users learn to use the molecular modeling programs available from the Computational Chemistry and Molecular Modeling Lab. These tutorials are actually the labs used for the course Pharmacy 491 - Introduction to Molecular Modeling. Reasonable efforts have been made to make these tutorials as free of errors as possible. However, if you find errors or have suggestions to make them more clear, please forward your comments to Dr.Peter Gannett (pgannett@hsc.wvu.edu).

Amber

Amber Files and Setup

Modeling Small Molecules

Building DNAs for Modeling

Building DNAs with Base Pair Mis-matches

DNA MD and Analysis

Proteins - MM and MD

Insight

Building Molecules in Insight

Protein setup, MM and MD

Homology Modeling and Docking

Sybyl

Building DNAs and Energy Minimization

Quantum Mechanics

Tools

Rasmol, Moil-View, and VMD

McSym for Novel DNA and RNA Structures

Utilities

Unix - the basics

Backing up files to tape

 

 
Several laboratory exercises have been prepared to help users learn to use the molecular modeling programs available from the Computational Chemistry and Molecular Modeling Lab. These labs used for the course Pharmacy 491 - Introduction to Molecular Modeling. Reasonable efforts have been made to make these tutorials as free of errors as possible. However, if you find errors or have suggestions to make them more clear, please forward your comments to Dr.Peter Gannett (pgannett@hsc.wvu.edu).

CCMM Lab

Brief Description
Introduction to Unix. Basic commands, directory management, filters, the shell, background processing, text editors, and a quick reference guide.
Modeling Input and Output files for Amber. How to generate, manipulate, use, and print them in.
Building and energy minimization of small molecules in Amber. Molecules built and minimized are methane, butane, and 1,2-dimethylcyclohexane. Pitfalls of energy minimization are pointed out.
Building DNAs, solvating, adding ions, and useful auxiliary programs for Amber are demonstrated in this lab. The example is d(A)10:d(T)10.
Building molecules InsightII and energy minimization.
Building DNAs and energy minimization with Sybyl.
Building DNAs with Base-Pair Mis-matches and Minimizing their Energy. Mis-matches include G:T, G:G, and G:A all in the Dickerson dodecamer.
Building, modification, energy minimization, and molecular dynamics of proteins using InsightII.
This lab is on the setup and molecular dynamics and analysis of DNA. The DNA is built (d(A)10:d(T)10), solvated, ions added, energy minimization by molecular mechanics, molecular dynamics run and then some analysis of the data is describe.
Setting up Proteins with substrates, conducting energy minimization and molecular dynamics, and analyzing the results with Amber (sander and carnal).
Introduction to Homology Modeling and Docking as Insight does it.

Tools and Utilities

Brief Summary

Display and Printing Structure Files

Three programs used for the display and printing of files generated by molecular mechanics and molecular dynamics are described and compared - Rasmol, MoilView and VMD

Building Novel DNA and RNA Structures

Anything but the generic DNA or RNA structures can be difficult to build. McSym was designed to handle this (eg loops, buldges, triplex DNA).

Backing Up and Archiving Files

Back up those monstrously large molecular dynamics files to tape. This document will tell you how to back up your files to tape using the tar (tape archiver) command.

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