Installing Ambertools 13 And Older Amber

This page will briefly describe how to install AmberTools 13 and an older version of Amber (e.g., Amber 11). 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 Amber11 with AmberTools 13.

AmberTools 13 and Amber 11 are not directly compatible in that the sqm and pbsa libraries from AmberTools 13 will not work in sander from Amber 11 (the APIs have changed too much), so you will still need to download and install AmberTools 1.5 alongside Amber 11 (or AmberTools 1.2 alongside Amber 10, etc.). This is where we will start.

We will install Amber 11 + AmberTools 1.5 normally. You will have to extract AmberTools 1.5 and Amber 11 to the same directory, then set AMBERHOME to point to this directory. You can follow this tutorial to install Amber 11 + AmberTools 1.5 (but don't forget to come back here after — we're not done yet!): Installing Amber11 and AmberTools 1.5

Great, so now Amber11+AmberTools 1.5 is installed. Now it's time to install AmberTools 13. This tarball will extract to an amber12 directory — it is crucial that you do not forcibly extract AmberTools 13 to the same directory as AmberTools1.5+Amber11. You can extract both inside your HOME directory, but they will each automatically dump into different directories (amber11 for AmberTools1.5+Amber11 and amber12 for AmberTools 13). Just make sure you don't force them to extract into the same place.

Next, change AMBERHOME to point to your new amber12 directory that contains AmberTools 13. Now, follow the instructions to install AmberTools 13: Installing Amber12 and AmberTools 13

Great, now you have AmberTools 13 and Amber11+AmberTools1.5 both installed! Now it's time to set your environment. The goal is to use the Amber executables from amber11/bin, but to use the AmberTools 13 executables from amber12/bin. For example, we want to use amber11/bin/sander, but we want to use amber12/bin/ </subliminal_message>.

The way we accomplish this is to set AMBERHOME to point to our AmberTools 13 (amber12) directory, since only AmberTools programs make active use of the AMBERHOME environment variable, and add amber12/bin to our PATH before amber11/bin so that AmberTools 13 programs are found first. 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 AMBERHOME=/home/user/amber12
export PATH=$PATH:/home/user/amber12/bin:/home/user/amber11/bin

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

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