SIMULATION IN CHEMISTRY & BIOCHEMISTRY

Chemistry 430

Spring Term 2019

Instructor: Jay Ponder


GENERAL INFORMATION

Syllabus & Schedule [PDF]


LECTURE SUMMARIES

Lecture 1 (Jan 17): Overview of Molecular Modeling [PDF]

Lecture 2 (Jan 22): Introduction to Molecular Mechanics I [PDF]


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

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]

FFE: Force Field Explorer

Force Field Explorer 8.5.3 Software for MacOS [DMG]

Force Field Explorer 8.5.3 Software for Windows [ZIP]

Force Field Explorer 8.5.3 Software for Linux [GZIPPED SH]

Force Field Explorer Manual [PDF]

Tinker: Software Tools for Molecular Design

Tinker 8.5.3 Software for MacOS [GZIPPED TAR]

Tinker 8.5.3 Software for Windows [ZIP]

Tinker 8.5.3 Software for Linux [GZIPPED TAR]

Tinker Manual [PDF]

Spartan Molecular Modeling (Q-Chem)

Spartan Student Overview [PDF]

Spartan Student Tutorial [PDF]

Walking Through Spartan Student (input file for tutorial) [Input]

Spartan '14 Manual [PDF]

Q-Chem 4.1 Manual [PDF]

Gaussian Quantum Chemistry

Gaussian 09 Online Manual [HTML]

GaussView 5 Online Manual [HTML]

APBS: Adaptive Poisson-Boltzmann Solver

PDB2PQR Command Line Usage [HTML]

APBS Command Line Usage [HTML]

APBS Input Files & Options [HTML]

pKa Calculations in APBS [HTML]

Tutorial: APBS, PDB2PQR, PyMol and VMD [HTML]

Tutorial: Lysozyme pKa Example for PDB2PQR [HTML]

SDA7 (Simulation of Diffusional Association, V7)

SDA7 Documentation [HTML]


LABORATORY PROJECTS

Suggested Lab Report Format [PDF]

Lab 1 (Jan 18): Unix Tutorial; Using Chimera, VMD, FFE & Spartan [Files]