Compiling AMBER Tools so you can start making input and analyzing output

So, you want to run simulation using AMBER? Well, first you'll need to generate some input files and for that - you need to use (x/t/s)LeaP. LeaP and other useful AMBER subprograms are now housed in the SVN repository in the $SVN/trunk/AMBERTOOLS directory. If you have not got this directory, running svn update from the top of the directory tree should add it for you. If you need to get the whole repository, take a look at the group SVN setup page.

Using AMBER can be broken down into simple stages:

1. Generate your input files
2. Symmetrise your topology file
3. Run your simulation (using GMIN/OPTIM or just plain AMBER)
4. Analyse your output

This tutorial deals with compiling the tools required for 1 and 4. Points 2 and 3 are covered in other tutorials that you can find here:

Once you have compiled AMBERTOOLS, you can learn how to produce input by taking a look at simple LeaP input scripts here: