Ok, i found the nab file and it is correct, exactly as you
proposed.....somehow when it creates the .c the \ disappears!!!!
George
> Hello,
>
> The .c file is created by nab2c, and is not the file you have to alter.
> Find where this comment is made in the corresponding nab file and change
> it there. grep is your friend here.
>
> Good luck!
> Jason
>
> --
> 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 - 09:00:03 PDT
