On Fri, Apr 9, 2010 at 6:40 PM, Ibrahim Moustafa <I.moustafa.psu.edu> wrote:
> Dear all,
>
> I managed to install AmberTools 1.3 on my Mac Osx 10.4 PPC following the
> installation guide and after using ³-g95² option.
> Also, I applied the ³bugfixall² after installation. However, I ran through
> two issues:-
>
> 1) In doing the test the following did not pass
> -----------------------------------------------------------
>> Running test to do simple lmod optimization
>
> 1c1
> < Glob. min. E = -128.257 kcal/mol
> ---
>> Glob. min. E = -135.830 kcal/mol
> FAILED (probably OK if energy is -120 to -130)
> ---------------------------------------------------------------
> Q: Is that usual to see such a difference in the test?
>
> 2) The ptraj is unable to read the .gz trajectory file. However, it works Ok
> with the unzipped file.
> I get the following error message in the case of .mdcd.gz file
>
> ----------------------------------------------------------------------------
> ---------------------------------
>> readAmberRestart(): sscanf on atoms and time in restart file
> filename.mdcrd.gz failed
> ----------------------------------------------------------------------------
> -----------------------------------
>
> Q: Has anybody come across this before? Any suggestion to solve this
> problem. It is more convenient to deal with the .gz rather than the unzipped
> file.
True, but it is even more convenient to deal with netcdf rather than
even a gzipped mdcrd. However, on to the problem:
The error message tells you that it's trying to open that file as a
restart, which is not what you want. What does your ptraj script look
like?
If it tries to open the file as a gzipped mdcrd, then it should work fine...
Good luck!
Jason
>
> Many thanks in advance for your help.
>
> Thanks,
> Ibrahim
>
>
>
>
>
>
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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 Fri Apr 09 2010 - 16:30:02 PDT
