Hi Gordon,
Does Amber10 not install successfully, or does it simply not pass all of the
tests? In any case, describing what happens is not as helpful for us as
exact transcript of what happened on the command-line itself. Can you
provide us with the error messages that popped up when you built Amber10?
On the other hand, if Amber10 built OK, and just some of the tests failed,
it would be helpful to see a log of which tests failed so we may be able to
say whether or not they're OK.
Note that you should not worry about any failures or errors in AmberTools
1.2 (built alongside Amber10), especially for tleap. There were a number of
segfaulting issues in tleap from AmberTools 1.2 that Mengjuei fixed for
AmberTools 1.3 and greater, so you should just use the AmberTools programs
shipped with AT 1.5 (which you can build alongside Amber11).
HTH,
Jason
On Fri, Jun 10, 2011 at 11:02 AM, Gordon Freeman <gfreeman.wisc.edu> wrote:
> Hello :)
>
> A few months ago, our research group acquired an Amber license for
> both Amber11 and Amber10 (amber10 for use with the PLUMED plugin). We
> have had no issues using Amber11 but the Amber10 installation resulted
> in failures in many of the testing cases (compared to 0 failures for
> the Amber11). Note that the Amber10 installation problems were
> encountered doing a simple installation of Amber10 alone; this
> installation was not done with the PLUMED plugin so we can rule out
> PLUMED as the source of the error. These errors also occurred in
> spite of using the bugfix.all file located athttp://
> ambermg.org/bugfixes10.html
> . Is there a common reason for such faulty installations? Perhaps an
> incompatibility between AmberTools and Amber10 or something like this
> we should be aware of?
>
> It would be optimal if the PLUMED package interfaced with Amber11 but
> as this is not yet the case, we would love to get Amber10 up and
> running for our research needs. Any advice you might have for getting
> Amber10 running properly would be most appreciated. Thanks!
>
> -Gordon
> Gordon Freeman
> Research Assistant
> Molecular Dynamics and Statistical Mechanics Research Group
> University of Wisconsin-Madison
> http://www.engr.wisc.edu/groups/mtsm/index.shtml
> gfreeman.wisc.edu
> 617.960.6165
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Jun 10 2011 - 22:00:02 PDT
