The ptraj file looks like that:
> trajin filename.mdcrd.gz 4000 5000 1
> reference file.pdb
> rms reference :1-470.CA
Similar scripts were working just fine with lower versions.
Also, It works Ok with the unzipped file.
Is there a way to tell ptraj that the file is a trajectory "gzipped" file
more than the extension mdcrd.gz?!!
Thanks for help,
Ibrahim
On 4/9/10 7:02 PM, "Jason Swails" <jason.swails.gmail.com> wrote:
> 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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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Fri Apr 09 2010 - 16:30:04 PDT
