Re: [AMBER] amber11 installation bugfix problem

From: Jason Swails <>
Date: Thu, 27 Jan 2011 07:12:59 -0500

I'm guessing you're using the "sudo" command to do stuff in the amber11
directory, since it's located in a (traditionally root-controlled)
directory: /usr/local.

The implications of this have been extensively discussed in the very recent
past on this list, with the ultimate conclusion being that this is a *bad*
idea, due to what the spawned root shell does and/or does not inherit from
the shell that launched it.

Your two options are: use "sudo -E " when applying bugfixes so that the root
shell inherits your environment variables.

My personal suggestion, change the ownership of your amber11 directory to
your user name and *DON'T* use sudo at all (except as needed to change
ownership, of course).

sudo chown -R `whoami` /usr/local/amber11

Then apply bug fixes as normal.

All the best,

On Thu, Jan 27, 2011 at 5:31 AM, Julia Romanowska <> wrote:

> Hi,
> I am trying to install Amber11 and I have a problem with applying bufixes.
> I have set the AMBERHOME:
> [amber11]$ echo $AMBERHOME
> /usr/local/amber11
> but the script is complaining:
> [amber11]$ sudo ./apply_bugfix.x bugfix.all
> Applying all bugfixes in AMBERHOME=/usr/local/amber11
> AMBERHOME environment variable not set.
> Cannot continue.
> I have noticed that the script is written in bash, so I have added to
> /etc/bashrc the setting of $AMBERHOME, but it still doesn't work.
> Maybe I'm making some stupid mistake... Could anybody help me?
> Best,
> Julia Romanowska
> ======================
> PhD student, Biophysics,
> Faculty of Physics
> and
> Interdisciplinary Centre for
> Mathematical and Computational
> Modelling (ICM),
> University of Warsaw, Poland
> tel.: +48 22-5540-832
> fax.: +48 22-5540-801
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Thu Jan 27 2011 - 04:30:04 PST
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