Re: [AMBER] Binding energy using

From: Jason Swails <>
Date: Thu, 6 Nov 2014 16:55:10 -0500

On Thu, Nov 6, 2014 at 4:50 PM, Aron Broom <> wrote:

> suggests you don't have libnetcdf installed, or not the right version for
> your AMBER install.
> Are you in linux? If so can you use your package manager to install
> libnetcdf?
> Or maybe you already have the library but it's in an unexpected location
> and needs to be added to the LD_LIBRARY_PATH environment variable.

​I suspect this is the case. Recent developments in Amber have
necessitated the use of shared libraries which get dumped in
$AMBERHOME/lib. As a result, there is a requirement that this location be
added to LD_LIBRARY_PATH. In upcoming versions with improved Python
integration, it will become necessary to augment PYTHONPATH as well.

Since the environment is getting trickier (or at least there are more
things needed) to set up correctly for Amber, the decision was made for the
AmberTools 14 release to generate a set of environment scripts --
and amber.csh -- that you can (and should) source directly in your shell or
in your login script to automagically set the environment variables that
need to be set.

So to Sook -- try adding the command:

source /*/amber14/

to your .bashrc file (or "source /*/amber14/amber.csh" to your .cshrc file
if you use cshell). Obviously, replace /* with your actual path.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Thu Nov 06 2014 - 14:00:03 PST
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