Hello,
Dan is right, you need to extract AmberTools 1.3 to amber11 directory
and amber10 directory to different places. This doesn't present much
of a problem, however. I would assign AMBERHOME to the AmberTools
directory, as I believe only certain AmberTools applications actually
make use of that environment variable (i.e., it's unnecessary for
AMBERHOME to point to the amber10 directory for sander, pmemd, and
other amber programs, but I think for nab it is important, though I
may be corrected here). For those programs that don't make explicit
use of the variable, as long as they are in the path you can execute
them just fine (or you can specify the full path of the executable).
One thing you probably should do is set AMBERHOME to each directory as
you install it (but I think that's actually done in the configure
script for both AmberTools and amber10). Bear in mind that you can
also reset AMBERHOME as needed (but you can't access sander as
$AMBERHOME/exe/sander if AMBERHOME points to your AmberTools 1.3
location, just keep that in mind).
Good luck!
Jason
On Tue, Jan 12, 2010 at 9:47 AM, Stefan weber
<stefan.weber.rz.uni-freiburg.de> wrote:
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> Hi Dan,
>
> will try so, but where should $AMBERHOME point to? Amber10 or like
> ambertools amber11?
> I'll try with both and tell you later on...
>
> Best
>
> Stef
>
> On 1/12/10 3:32 PM, Daniel Roe wrote:
>> Hi Stefan,
>>
>> I'm not 100% certain, but since AmberTools 1.3 contains many
>> updates to the configure/compile process (one of the reasons it
>> extracts to amber11) it's likely that it is not completely
>> compatible with the amber 10 install process. Try to keep the two
>> separate and see if you can do a fresh install of amber10 by
>> itself, in its own directory.
>>
>> -Dan
>>
>> Stefan weber wrote: Hello,
>>
>> just a complete newbie with amber. I tried to install amber10 on
>> ubuntu 9.10 64bit. and got follwing problem. compiling starts
>> (amber -- ambertools v 1.3 are already done and tests are fine),
>> running a while and stopping with error do not find lapack.a and
>> blas.a. Both files where created just before and moved to the
>> $AMBERHOME/lib directory. Any help?
>>
>> Ok there are some other strange things before. All documentation
>> telling me ambertools and amber should be unpacked in one
>> directory, trying to do so amber10 extracts in amber10 and
>> ambertools1.3 in amber11. So to put them in one directory I
>> unpacked amber10 (to /usr/local/amber10) renamed folder amber10 to
>> amber11; unpacked ambertools and renamed the stuff back to amber10,
>> setting environment ($AMBERHOME) and PATH pointing to
>> /usr/local/amber10, then I patched everything (first ambertools
>> then amber10 and then starting to compile. As said before
>> ambertools v 1.3 compiled fine, run ambertools tests fine and then
>> run into trouble compiling amber10.
>>
>> I attached the logfile from compiling amber10 ( make serial >>
>> make-serial.log 2>&1 )
>>
>> Any Help?
>>
>> -- Stefan Weber Tel: +497612034642
>>
>> Rechenzentrum der Universität Freiburg Hermann-Herder-Str. 10
>> D-79104 Freiburg
>>
>> ++ Das Leben -- so wie es wirklich ist -- ist nicht der Kampf
>> zwischen Gut und Böse, sondern zwischen Böse und noch Schlimmerem.
>> ++
>>>
>
> - --
> Stefan Weber
> Tel: +497612034642
>
> Rechenzentrum der Universität Freiburg
> Hermann-Herder-Str. 10
> D-79104 Freiburg
>
> ++ Das Leben -- so wie es wirklich ist --
> ist nicht der Kampf zwischen Gut und Böse,
> sondern zwischen Böse und noch Schlimmerem. ++
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--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Tue Jan 12 2010 - 07:30:03 PST
