SIMULATION IN CHEMISTRY & BIOCHEMISTRY

Chemistry 430

Spring Term 2020

Instructor: Jay Ponder


GENERAL INFORMATION

Syllabus & Schedule [PDF]


LECTURE SUMMARIES

Lecture 1 (Jan 13): Overview of Molecular Modeling [PDF]

Lecture 2 (Jan 15): Introduction to Molecular Mechanics I [PDF]

Lecture 3 (Jan 22): Introduction to Molecular Mechanics II


READINGS & REFERENCES

Introduction to Using a Linux Terminal Window

Unix for the Beginning Mage, J. Topjian [PDF]

Useful Unix/Linux Tools [HTML]

Perspectives on Molecular Modeling

Biomolecular Modeling: Goals, Problems, Perspectives,
W. F. van Gunsteren, D. Bakowies, R. Baron, I. Chandrasekhar, M. Christen,
X. Daura, P. Gee, D. P. Geerke, A. Glattli, P. H. Hunenberger, M. A. Kastenholz,
C. Oostenbrink, M. Schenk, D. Trzesniak, N. F. A. van der Vegt and H. B. Yu,
Angewandte Chemie International Edition, 45, 4064-4092 (2006) [PDF]

Biomolecular Modeling and Simulation: A Field Coming of Age,
T. Schlick, R. Collepardo-Guevara, L. A. Halvorsen, S. Jung and X. Xiao,
Quarterly Reviews of Biophysics, 44, 191-228 (2011) [PDF]


SOFTWARE RESOURCES

General Information

How to Install Non-AppStore Programs on MacOS [PDF]

How to Disable the (Annoying!) Gatekeeper on MacOS [PDF]

Avogadro & Avogadro2: Molecular Editors

Avogadro 1.2.0 Software for MacOS [DMG]

Avogadro 1.2.0 Software for Windows [EXE]

Avogadro2 1.91 Software for MacOS [DMG]

Avogadro2 1.91 Software for Windows [EXE]

Learning Avogadro [PDF]

Avogadro Example Files [GZIPPED TAR]

Chimera: Extensible Molecular Modeling System

Chimera 1.13 Software for MacOS [DMG]

Chimera 1.13 Software for Windows [EXE]

Chimera 1.13 Software for Linux [BIN]

Chimera Quick Reference [PDF]

Chimera Getting Started [HTTP]

Chimera User's Guide [HTTP]

PyMOL: Python-Enhanced Molecular Graphics

PyMOL 1.7.4.5 Software for MacOS [DMG]

PyMOL 1.7.4.5 Software for Windows [MSI]

PyMOL 1.7.4.5 Software for Linux [GZIPPED TAR]

PyMOL Quick Reference [PDF]

PyMOL Introduction [PDF]

PyMOL Tutorial [PDF]

PyMOL User's Guide [PDF]

VMD: Visual Molecular Dynamics

VMD 1.9.4 Software for MacOS [DMG]

VMD 1.9.3 Software for Windows [MSI]

VMD 1.9.4 Software for Linux [GZIPPED TAR]

VMD User's Guide [PDF]

Using VMD Tutorial [PDF]

VMD Tutorial Files [GZIPPED TAR]


LABORATORY PROJECTS

Suggested Lab Report Format [PDF]

Lab 1 (Jan 17): Unix Tutorial; Using Chimera, VMD, FFE & Spartan [Files]