Re: [AMBER] Error Compiling NAB o AMBER Tools 1.2

From: Jason Swails <jason.swails.gmail.com> Date: Wed, 14 Jul 2010 15:18:53 -0400

--
Jason Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
On Jul 14, 2010, at 11:44 AM, "Giorgos Lamprinidis" <lamprinidis.pharm.uoa.gr> wrote:
> 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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> 
> 
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