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
>>
>>
>>
>> _______________________________________________
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>> 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
> _______________________________________________
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>
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Received on Wed Jul 14 2010 - 08:00:03 PDT
