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.
cd ~/svn svn update
If you need to get the whole repository, take a look at the group SVN setup page. This tutorial assumes that you have followed those directions exactly, and your SVN directory is ~/svn. If this is not the case, please modify all paths accordingly.
Using AMBER can be broken down into simple stages:
- Generate your input files
- Symmetrise your topology file
- Run your simulation (using GMIN/OPTIM or just plain AMBER)
- 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:
Compiling AMBER Tools
Compiling AMBER Tools is very easy, but it can take a while - over 10 minutes. Luckily, you will only need to do this once unless major bug fixes are introduced. Keep an eye on the SVN RSS feeds for more information.
First, you need to change into the AMBER Tools source directory:
cd ~/svn/AMBERTOOLS/src
Now you need to set the $AMBERHOME environment variable to point to your AMBERTOOLS directory:
vi ~/.bashrc
Insert the following (ideally replacing $USER with your user name!):
export AMBERHOME=/home/$USER/svn/AMBERTOOLS
Exit vi and then source the file you just altered to export the new variable:
source ~/.bashrc
As you're about to compile some code, it is worth checking that you have some compilers loaded. If you are not sure, try:
module load compilers
Next you need to configure the installation to your environment using the configure script provided:
./configure_at gcc