Installing AmberTools 15 And Older Amber

This page will briefly describe how to install AmberTools 15 and an older version of Amber (e.g., Amber 12). These two packages can coexist together, and it's relatively straightforward to get them to coexist.

As an example (and because the bulk of the documentation has already been done), I will describe how to set up Amber12 with AmberTools 15.

AmberTools 15 and Amber 12 are not directly compatible in that the sqm and pbsa libraries from AmberTools 15 will not work in sander from Amber 12 (but now that sander is part of AmberTools, this no longer matters), so you will still need to download and install AmberTools 13 alongside Amber 12. This is where we will start.

We will install Amber 12 + AmberTools 13 normally. You will have to extract AmberTools 13 and Amber 12 to the same directory, then set AMBERHOME to point to this directory. You can follow this tutorial to install Amber 12 + AmberTools 13 (but don't forget to come back here after — we're not done yet!): Installing Amber12 and AmberTools 13

Great, so now Amber12+AmberTools 13 is installed. Now it's time to install AmberTools 15. This tarball will extract to an amber14 directory — it is crucial that you do not forcibly extract AmberTools 14 to the same directory as AmberTools13+Amber12. You can extract both inside your HOME directory, but they will each automatically dump into different directories (amber12 for AmberTools13+Amber12 and amber14 for AmberTools 14). Just make sure you don't force them to extract into the same place.

Next, change AMBERHOME to point to your new amber14 directory that contains AmberTools 15. Now, follow the instructions to install AmberTools 14: Installing Amber14 and AmberTools14

Great, now you have AmberTools 15 and Amber12+AmberTools13 both installed! Now it's time to set your environment. The goal is to use the Amber executables from amber12/bin, but to use the AmberTools 14 executables from amber14/bin. For example, we want to use amber12/bin/pmemd.cuda, but we want to use amber14/bin/cpptraj and amber14/bin/sander.

The way we accomplish this is to set the environment from AmberTools 15, and simply add the bin directory to Amber 12 in to the PATH. But it is important that the AmberTools 15 bin directory appears in PATH before that from Amber 12, so that the AmberTools 15 programs are executed when run on the command-line.

The key here is to modify PATH to include Amber 12, then source the resource script for AmberTools 15.You can add this to your .bashrc file to make this occur automatically on login (or .cshrc for csh and its derivatives).

This would look like:

export PATH=/home/user/amber12/bin:${PATH}
source /home/user/amber14/ # Use amber.csh for C-shell derivatives

This assumes that the installations are located in /home/user — change this to the real installation location.

Unless otherwise stated, the content of this page is licensed under Creative Commons Attribution-ShareAlike 3.0 License