Re: [AMBER] Error installing Ambertools on Centos 6.3 and open suse 12.3

From: Jason Swails <>
Date: Thu, 17 Jul 2014 08:11:46 -0700

On Thu, Jul 17, 2014 at 5:45 AM, Charu Suri <> wrote:

> Dear Amber Users,
> I'm trying to install Ambertools1.3 along with Amber11 on Centos 6.3 and
> open suse 12.3. However I am getting the following errors for serial
> installation itself :
> /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld:
> cannot find -ldrfftw
> /usr/lib64/gcc/x86_64-suse-linux/4.7/../../../../x86_64-suse-linux/bin/ld:
> cannot find -ldfftw
> collect2: error: ld returned 1 exit status
> cc failed!
> make[1]: *** [matextract] Error 1
> make[1]: Leaving directory
> `/home/bioinfo6.corp/Projects/test/amber/AmberTarFiles/amber11/AmberTools/src/nss'
> make: *** [serial] Error 2
> Please find attached the complete error log.
> I could successfully install the same packages in Ubuntu. However, due to
> existing system limitations, I need to install the same on Centos or Open
> suse.
> Awaiting response.

‚ÄčAmberTools 1.3 is not compatible with Amber 11 if I recall correctly. You
need AmberTools 1.4 or AmberTools 1.5.

That said, these are very old versions of Amber (from 2010) that are no
longer supported. The last time I tried installing Amber 11, it did not go
smoothly and I had to keep making small changes in response to compiler
errors until I got it to compile.‚Äč

Please update to AmberTools 14 (which contains the 'sander' simulation
engine) and Amber 14 if you have need of pmemd or pmemd.cuda. If you
absolutely require Amber 11 for some reason, you will need to tweak the
Amber source code (and/or configure script) in response to the error
messages you get in order to fix error messages you get (Google is your
friend here).

Hope this helps,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Thu Jul 17 2014 - 08:30:02 PDT
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