Re: [AMBER] Amber 11 installation problems

From: Linus Johannissen <>
Date: Wed, 17 Nov 2010 22:34:53 +0000

Thanks Tru, but I did try both with and without first installing AmberTools (sorry I forgot to mention that!), and I get the same error when I run "make" in $AMBERHOME/AmberTools/src/.

This time I started over with a clean slate, trying just to install AmberTools. One thing I find perplexing is that even though I run "./configure intel", the first few lines when running make seem to suggest it's using f90, although later on it's using icc and ifort (no idea if this is normal):

cd netcdf/src && make install
make[1]: Entering directory `/home/linusj/amber/amber11/AmberTools/src/netcdf/src'
Making install in f90
make[2]: Entering directory `/home/linusj/amber/amber11/AmberTools/src/netcdf/src/f90'

Anyway, the only error message I can spot is the same as before:
chmod: cannot access `/home/linusj/amber/amber11/AmberTools/src/netcdf/lib/libnetcdf.a': No such file or directory
make[3]: *** [install-libLTLIBRARIES] Error 1
make[2]: *** [install-am] Error 2
make[1]: *** [install-recursive] Error 1
make: *** [../netcdf/lib/libnetcdf.a] Error 2

As always, thank you for your suggestions

Dr Linus Johannissen
Post-doctoral research associate
Manchester Interdisciplinary Biocentre
University of Manchester

From: Tru Huynh []
Sent: 17 November 2010 18:40
To: AMBER Mailing List
Subject: Re: [AMBER] Amber 11 installation problems

On Wed, Nov 17, 2010 at 05:44:21PM +0000, Linus Johannissen wrote:
> Thanks for the quick reply!
> Here are some more details:
> 1. I untarred Amber 11 and AmberTools 1.4 in /home/linusj/amber, and set $AMBERHOME to /home/linusj/amber/amber11
> 2. I applied the bug fixes for both Amber 11 and AmberTools 1.4
> 3. The directory /home/linusj/amber/amber11/AmberTools/src/netcdf/ was created, but it does not contain libnetcdf.a
> 4. Step-by-step, this was my procedure: 1) untar Amber and AmberTools; 2)
> apply the patches for Amber (apply_bugfix.x bugfix.all); 3) apply the patch
> for AmberTools (patch -p0 -N < bugfix.all) -- and no, I didn't use the same
> "bugfix.all" for both; 4) use "configure intel" in $AMBERHOME/AmberTools/src/
> to generate the config.h files;

you forgot to build ambertools
make && make install
(cd $AMBERHOME/test && make test)

before continuing


Dr Tru Huynh          | | tel/fax +33 1 45 68 87 37/19
Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15 France
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Received on Wed Nov 17 2010 - 15:00:03 PST
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