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Jason Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
On Jul 14, 2010, at 10:30 AM, "Giorgos Lamprinidis" <lamprinidis.pharm.uoa.gr> wrote:
> Jason
>
> Thanks for your comments.
>
> I re-downloaded ambetrtools 1.2 and re-patched the code.... i am getting
> the same error message.
> How shall i change the source code since the file na_anal.c is created by
> the makefile_at??? I did changed the file manually and when i run make -f
> Makefile_at the program re-created the wrong file...
> I also downloaded an evaluation version of icc compiler....and run the
> configure_at with icc, but....always the same error....
>
>
> Any help please....
>
> Dr. George Lamprinidis
>
>
>> Hello,
>>
>> My comments are below.
>>
>> On Wed, Jul 14, 2010 at 6:02 AM, Giorgos Lamprinidis <
>> lamprinidis.pharm.uoa.gr> wrote:
>>
>>> Dear amber users
>>>
>>> I am trying to compile AmberTools 1.2 to a new Linux machine having
>>> 64bit
>>> Intel Core2 vPro proc.
>>> 1) I patch the source code.
>>> 2) I run the configuration script using -gcc compiler.
>>> 3) I run the make -f Makefile_at script and i get the following error
>>> message:
>>>
>>> ./nab -c bdna.nab
>>> ./nab -c dg_helix.nab
>>> ./nab -c getchivol.nab
>>> ./nab -c getres.nab
>>> ./nab -c getseq_from_pdb.nab
>>> ./nab -c getxyz_from_pdb.nab
>>> ./nab -c -DBINDIR='"/opt/Amber10_tars/amber10/bin"'
>>> -DDATDIR='"/opt/Amber10_tars/amber10/dat"' getpdb_prm.nab
>>> ./nab -c getpdb_rlb.nab
>>> ./nab -c linkprot.nab
>>> ./nab -c link_na.nab
>>> ./nab -c -DDATDIR='"/opt/Amber10_tars/amber10/dat"' na_anal.nab
>>> na_anal.c:2417:41: warning: missing terminating " character
>>> na_anal.c: In function ‘helixanal’:
>>> na_anal.c:2417: error: expected ‘)’ before ‘is’
>>> na_anal.c:2417: error: stray ‘\’ in program
>>> na_anal.c:2417:40: warning: missing terminating " character
>>> na_anal.c:2417: error: missing terminating " character
>>> na_anal.c:2419: error: expected ‘;’ before ‘}’ token
>>> cc failed!
>>> make[1]: *** [na_anal.o] Error 1
>>> make[1]: Leaving directory `/opt/Amber10_tars/amber10/src/nab'
>>> make: *** [install] Error 2
>>>
>>>
>>>
>>> When i search the na_anal.c file i see at line 2417 the following:
>>> 2416 else{
>>> 2417 printf( "\"%s" is not a valid answer.\n", ParallelAnswer );
>>>
>>
>> This looks strange. The way it's written, the first " is ended after %s".
>> To fix this, add a \ before that ". The line will look like this after
>> you're done:
>>
>> printf( "\"%s\" is not a valid answer.\n", ParallelAnswer );
>>
>> It seems very strange that this would not have been fixed, though. Maybe
>> the file became corrupted somehow? Did you apply all of the bug fixes?
>> It
>> may be worth untarring a new copy of AmberTools-1.2, because this is a
>> very
>> strange error to be getting. However, you can also make the above fix,
>> see
>> if it compiles, and then see if it passes the tests.
>>
>> In any case, you can also install AmberTools-1.4 afterwards (though I know
>> AT 1.2 is needed for Amber10).
>>
>> Good luck!
>> Jason
>>
>>
>>> 2418 NotValidAnswer = 1;
>>> 2419 }
>>>
>>> As i figured out the na_anal.c is produced during the make procedure, so
>>> how can i bypass this error?
>>>
>>> Thanks for your time.
>>>
>>> Dr George Lamprinidis
>>>
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>>
>> --
>> Jason M. Swails
>> Quantum Theory Project,
>> University of Florida
>> Ph.D. Graduate Student
>> 352-392-4032
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
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Received on Wed Jul 14 2010 - 08:30:06 PDT