Learning the Unix Command-line
A basic knowledge of how to navigate a filesystem, execute
commands, and to create files and folders is a prerequisite to understanding
the rest of the Amber tutorials. Basic competencies in Unix and command-line
interfaces are part of a core computing proficiency and will serve you well
in other pursuits. Increasing fluency will ensure that you get the most out
of the content offered on this site.
The link provided at the top navigates to an interactive Unix tutorial
through Codecademy, and is ideal
for beginners. You will need to create a free login to use it. There are
many other resources for Linux and Unix, but this is in the right
(No affiliation with AMBER)
Fundamentals of LEaP
This tutorial demonstrates rudimentary
system building in LEaP, the main program for preparing simulations in AMBER.
The tutorial serves as a nice reference for different kinds of files used in
the LEaP program, introduces the workflow, and provides a simple example of
building a protein in water.
By Pengfei Li and David Cerutti
TUTORIAL B0: An Introduction to
Molecular Dynamics Simulations with AMBER
This tutorial is designed for new users who have little or
no experience with running molecular dynamics simulations. It assumes no
prior knowledge of AMBER or Linux but assumes that AmberTools 14 as well as
VMD are correctly
installed on your system and AMBERHOME is set correctly. If you are new to
AMBER and MD in general this is the place to start.
By Ben Madej and Ross Walker
TUTORIAL B1: Simulating a small
fragment of DNA
will act as a basic introduction to LEaP, sander and ptraj, to build,
solvate, run molecular dynamics and analyze trajectories. It will also cover
visualising trajectories using
VMD. The aim of this
tutorial is to act as a brief introduction to running classical molecular
dynamics simulations using the AMBER software.
In this tutorial we will create a initial structure for a 10-mer of DNA
and then we will run gas phase, implicit and explicit solvent
simulations on it. Finally we will look at a practical example of how MD
simulations can be used to investigate how A-DNA can convert to B-DNA.
TUTORIAL B2: Using VMD with AMBER
tutorial acts as a brief introduction to using
VMD for visualising AMBER
inpcrd, restrt and trajectory files. While only scratching the surface of
what VMD can do it covers setting up a .vmdrc file to set the default layout
of VMD, loading static structures and performing RMSD fits between similar
structures. It then goes on to cover loading and visualising AMBER
trajectories, both from gas phase/implicit solvent simulations and from
periodic boundary simulations and shows how to save individual frames from a
trajectory as well as create an MPEG video of the trajectory.