BCMB/CHEM 8200 Molecular Modeling and Structure Computations

Coordinator: Dr. R. Woods (2-4454)
Office hours: Wed and Fri only 9:30 AM - 11:30 AM
Contributor: Dr. J. Wampler (2-1573)
Office Hours: Mon and Fri only 10:00 AM - 12:00 AM

Tuesdays and Thursdays (9:30-10:45)------- Chemistry Room 557 (MGL)
Text: Molecular Modeling Principles and Applications
Author: A. R. Leach, Longman Press, 1998

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GRADING:

               Assigned Labs (4) 5%/each                Exam #1 35%
               Research Presentation 25%                Exam #2 20%

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CLASS SCHEDULE

Lecture schedule

Dr. Wampler's Lecture Notes On-Line

Different Concepts of Molecular Structure

Size Matters

Intra- and Inter-molecular Forces

Hydrogen Bonds in Biochemistry

Molecular Mechanics and Force Fields

Using a Molecular Mechanics Force Field

Minimization and Optimization

Parameters for Molecular Mechanics

Water models for Molecular Mechanics

Dr. Wampler's Lab Sessions and Exam:

Notes and Tutorial for First Laboratory Session

Notes and Instructions for Second Laboratory Session

Study points for the first quiz

Notes and Instructions for Third Laboratory Session

Dr. Woods' Lecture Notes On-Line

Introduction to Course

Computational Methods

Considerations in Multi-molecular Simulations

Further MD-related Issues

Dr. Wood's Lab Sessions and Exam:

Notes and Instructions for Min/MD in vacuo lab

Notes and Instructions for solvated MD lab

Dr.Oren M. Becker' Site for his Course in Theoretical and Computational Chemistry of Biological Macromolecules

An Introduction to Unix and Your account: Unix Nuts and Bolts
Web Tutorials: "To-the-Web, To-the-Web"
A Summary of simple HTML codes
Examples of student Web-based Lab Report