Re: [AMBER] update ambertools

From: Kevin Keane <>
Date: Wed, 2 May 2018 10:20:30 -0700

As an additional tip: for Linux systems that support modulefiles, you can
use that mechanism to switch easily between versions of Amber. On RedHat,
you have to install the environment-modules RPM to support it; other
distributions probably have a similar mechanism.

With modulefiles set up, you can then easily switch between the version of

module load amber/12 - will set up all your paths for Amber 12.
module load amber/18 - will set up all your paths for Amber 18
module load amber - will set up all the paths for the version of Amber
listed in .version

module unload ... (same arguments as module load) will clean up all the
environment variables.

Other interesting module commands:

module avail
module show amber

Here is how to set it up (for Amber 16 in my example - add files named 12
for Amber 12, 18 for Amber 18, and so on):

Remove all Amber-related environment variables from your PATH, bashrc, etc.

Then create a directory /etc/modulefiles/amber. In this directory, create a
file for each version of Amber you wish to support. For instance, for Amber
16, I have a file called "/etc/modulefiles/amber/16" with the following

#%Module 1.0
# Amber 16 module for use with 'environment-modules' package:

module load openmpi

prepend-path PATH /opt/amber/amber16/bin
setenv PYTHONPATH /opt/amber/amber16/miniconda
prepend-path PYTHONPATH
setenv AMBERHOME /opt/amber/amber16
setenv AMBERPREFIX /opt/amber/amber16
prepend-path LD_LIBRARY_PATH /opt/amber/amber16/lib

In your situation, you could create one file called 12 and one file called
18, with the corresponding paths.

Add one file called "/etc/modulefiles/amber/.version" (notice that this is
a dotfile - there is a leading dot before the word version), with this
content (change the version of Amber as needed):

## The desired version of Amber
set ModulesVersion "16"

Kevin Keane | Systems Architect | University of San Diego ITS |
Maher Hall, 192 |5998 Alcalá Park | San Diego, CA 92110-2492 | 619.260.6859

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On Wed, May 2, 2018 at 5:26 AM, David A Case <> wrote:

> On Wed, May 02, 2018, Tousif Hossen wrote:
> >
> > Currently I am using Amber12 with Ambertools12. now I just want to
> > update my Ambertools12 to Ambertools15. so, is Amber12 compatible
> > with Ambertools15? can I update my Ambertools?
> You should install AmberTools18, which will download into a folder named
> "amber18". Point your AMBERHOME variable to that directory, and add
> $AMBERHOME/bin to your PATH.
> When you wish to run pmemd (which is the only program in Amber12 that is
> not contained in AmberTools18), simple give the full path to that
> executable (e.g. /somewhere/amber12/bin/pmemd) when you run it.
> (pmemd does not make use of the AMBERHOME environment variable)
> Amber12 is now six years old, which is old in dog-years. You should
> consider upgrading to Amber18 if you plan to run long or expensive
> simulations. Fee waivers may be available; please visit
> for more information.
> ....dac
> _______________________________________________
> AMBER mailing list
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Received on Wed May 02 2018 - 10:30:02 PDT
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