Introduction to Molecular Modeling

Fall Semester, 2016

Professor Emeritus Ray Fort Jr.

252 Aubert Hall


Course Materials
Syllabus Exercises Example Project Reports
Questions and Answers Frost's Circle Software and Documentation
Tips and Tricks Simple Huckel Calculator Remote Access to Workstations
Weekly Appointment Schedule

Molecular Mechanics
Methodology Projects Models

Basics for MO Theory
Working with p-MOs LCAO Methods Orbital Interactions
Quantum Mechanics Electron Correlation Density Functional Theory
Symmetry Solvation Energy Comparisons
Problem Solving - An Example   Be a Quantum Mechanic!

Earn Big Bucks!

Semi-Empirical MO Calculations
Methodology Projects References
Jimmy Stewart's MOPAC Semiempirical Program
(Free academic license)
Tricks for Working with SPARTAN Spartan Keywords  

Ab Initio Calculations
Basis Sets Projects Reaction Energetics
Gaussian   References
PNL Database of
Basis Sets
An Annotated Gaussian Output File Frequency Scaling Factors

Range of Applicability Elements Relative Performance of Models

Docking Molecular Dynamics Homology Modeling
Official Tutorial: AutoDock (pdf) Tutorial: NAMD Tutorial: SwissModel/Modeller
Projects Projects Projects
Local AutoDock tutorial (pdf)

Part I

Part II

Autodock Video Tutorial

(Needs Adobe Flash Player)


General Information
UNIX Commands Computer Terms

This page last modified 10:31 AM on Wednesday November 16th, 2016.
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