Thanks Jason for the guild. It works for me now. :)
-Sook Wong
-----Original Message-----
From: Jason Swails [mailto:jason.swails.gmail.com]
Sent: Thursday, November 06, 2014 4:55 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Binding energy using mm_pbsa.pl
On Thu, Nov 6, 2014 at 4:50 PM, Aron Broom <broomsday.gmail.com> 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 -- amber.sh 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/amber.sh
to your .bashrc file (or "source /*/amber14/amber.csh" to your .cshrc file if you use cshell). Obviously, replace /* with your actual path.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Nov 07 2014 - 13:30:02 PST
