Re: [AMBER] bad atom type o

From: Jason Swails <>
Date: Wed, 20 Aug 2014 18:34:43 -0400

On Wed, Aug 20, 2014 at 5:36 PM, Hallel Freedman <>

> Jason,
> Yes I am getting:
> /global/software/amber/amber14/bin/sander: error while loading shared
> libraries: cannot open shared object file: No such file or
> directory
> Does this mean that there is a problem with the install?

​No, it simply means that you didn't source the Amber environment script
that was provided by configure. Try running the following command:

source /global/software/amber/amber14/

or if you use csh/tcsh:

source /global/software/amber/amber14/amber.csh

This should set up not only AMBERHOME and PATH, but LD_LIBRARY_PATH as well
(so the loader can find​ at runtime).

If you want your environment to be set up every time you start a shell, add
the source command to your shell resource file (e.g., ~/.bashrc, ~/.cshrc,
~/.zshrc -- whatever is the correct file for your shell on that machine).

Hope this helps,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Wed Aug 20 2014 - 16:00:03 PDT
Custom Search