Re: [AMBER] Compiling Ambertools 1.4 on MacBook SnowLeopard10.6.4

From: Jason Swails <>
Date: Thu, 11 Nov 2010 11:18:54 -0600

On Thu, Nov 11, 2010 at 10:37 AM, David Watson <> wrote:

> On Nov 11, 2010, at 10:19 AM, Dean Cuebas wrote:
> > <snip>
> > 4) I cd to the src directory of Ambertools and type
> > ./configure -macAccelerate gnu
> >
> > +++++++++++++++++++++++++++++++++++++++++++++
> > Your AMBERHOME environment variable should be set to /usr/local/amber11
> >
> >
> You may want to try compiling as root, if you are going to compile to
> /usr/local/amber11

A safer route suggested by Lachele that I've adopted: Change ownership of
/usr/local to a user that installs regularly, since /usr/local is typically
non-system-vital *stuff*. That way, you won't accidentally clobber anything
in / unwittingly, because you never *quite* know what scripts do. Of
course, there's no need to install amber in /usr/local, and I never do.

> Here's what I do when compiling amber:
> sudo -E -s
> You will now be root, and hopefully your environmental variables will be
> preserved; use plenty of caution.
> Follow the remaining instructions regarding installation of AMBER.
> When it comes time to run the tests, you may want to perform the following
> (as root):
> chown -R dean:staff /usr/local/amber11/test
> Note: change dean to whatever your short username is.
> Then when you go to run the tests, either exit the "root" session, or start
> a fresh terminal and change to the correct directory for performing the
> tests. It's a lot easier and safer to set up mpi as a normal user than to
> try to configure passwordless ssh as root.
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Thu Nov 11 2010 - 09:30:04 PST
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