Resources for Computational Chemistry

Not exhaustive, but a good place to start!

Introduction to Computational Chemistry
Theoretical Chemistry: a self-guided introduction for college students by Jack Simon at the University of Utah.
Introduction to Computational Chemistry by Dave Young on
Education: Computational Chemistry collection of links at ETHZ.
Electronic Structure Methods, a brief introduction, at the York Centre for Laser Spectroscopy.
A compilation of Lectures from the ACS PRF Summer School on Computation, Simulation and Theory in Chemistry.

Unix Tutorial for Beginners from the EE dept at Surrey.
Basic Unix commands (and More Unix) from Suzanne Riehemann at Stanford.

Text Editors
emacs Basics from Suzanne Riehemann at Stanford.
Basic vi commands from the CS dept at Colorado State.
The nedit program needs no tutorial. You can start nedit by typing ~jkua/bin/nedit or ~jkua/bin/nedit

Note: to figure out the pathway for line 1 in your perl script, type "which perl" at the Unix prompt.
Beginner's Introduction to Perl by Doug Sheppard at (Note: the series has five parts.)
Perl Tutorial at Leeds, UK.
Links to Perl websites compiled at CodeBox.

Software/Programs that we use
Rasmol viewer Command reference.
Schrodinger software: We are currently using Jaguar 6.0 for QM calculations and the Maestro interface. Manuals available in pdf format on my lab computers.
Molden can be coupled for pre- and post-processing ReaxFF and Gaussian.  It is useful for visualization and building molecules (see the Z-matrix editor).
Gaussian online manual from Gaussian (the '03 version), used for QM calculations. We have the older g98.
Amber home page at TSRI. We have Amber 9.0 running. (Amber is used for MD simulations of biological systems.)
Tinker molecular modelling software for MM and MD simulations.
VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems.
Autodock 3.0.5 online manual used for automated docking of ligands to protein receptors.
Pymol is much more versatile than Rasmol for viewing biological molecules.
Mercury for viewing Crystal Structures.

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