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 ccl.net
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/Linux
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
Perl
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 perl.com.
(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.