Re: [AMBER] ambertools14 fresh installation fails

From: Fabian Glaser <>
Date: Wed, 28 Jan 2015 15:01:24 +0200

Dear all,

I think the main problem was a shell definition of paths, I was unaware that I was using /bin/zsh shell, and the paths that in the .bash_profile were irrelevant, when I corrected that and updated the .zshrc file and UPDATED and the gfortran compiler (I had a different error there), the compilation of AmberTools at least went OK.

So I installed again the gnu compilers and updated as explained here

I got some very few warnings and a couple of error on make test, I pass them on since I upgraded to yosemite 10.10.2 this morning, maybe somebody else had similar problems.

I add the two logs here in case they are useful, but most of what I need in my local machine is OK. So problem solved.



So solved!!

Thanks a lot,


Fabian Glaser, PhD

Technion - Israel Institute of Technology
Haifa 32000, ISRAEL
Tel: +972 4 8293701
Fax: +972 4 8225153

> On Jan 28, 2015, at 12:12 AM, Jason Swails <> wrote:
> On Tue, Jan 27, 2015 at 3:35 PM, Fabian Gmail <>
> wrote:
>> Thanks Dac Jason,
>> I did removed completely the amber14 and amber12 old dirs before
>> attempting a fresh download and installation and I do have a
>> $AMBERHOME/.patches dir... Which I did not touch.
> ​Untarring a fresh AmberTools14.tar.bz2 or AmberTools13.tar.bz2 will not
> create a .patches directory. It is created the first time update_amber
> runs. A simple thing to do would be remove the .patches directory, but its
> very existence indicates that something is weird with your install process,
> and I don't know what.
> ​Where did you get the tarball? Downloaded from the Amber website? Does
> the md5sum match what the Amber website says it should?
> (589cc9bd17b15ce3f9604b0bdeea3bab)
> And you're sure you removed "amber14" and "amber12" before trying this?
> Is it possible you ran a command you thought removed everything that really
> didn't? (The only example here that comes to mind is running " rm -fr
> amber14/* " instead of " rm -fr amber14 "). By default, I think "rm -fr
> amber14/*" will not match any "hidden" dot-directories inside amber14 (like
> .patches).
> I've reached the point of pure conjecture at this point, since there must
> be *some* detail of your process that you are not reporting here (perhaps
> you don't even know that what you are doing is "different") that is causing
> these issues. The code in question (i.e., the part of update_amber that
> checks for existing updates) is quite robust and platform-independent (and
> routinely tested/used on Mac OS X, anyway), and the contents of the Amber
> release tarball are completely platform-independent. This almost
> completely precludes the root cause of this problem being Amber
> ​
>> ​​
>> Should I delete it too or its content (the .patches ) before and trying
>> again???
> ​Delete everything (the whole existing $AMBERHOME directories) and try
> extracting a fresh AmberTools14.tar.bz2 file whose md5sum you have verified
> matches the one I printed above.
> HTH,
> Jason
> ​
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Wed Jan 28 2015 - 05:30:05 PST
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