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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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Jul 14 2010 - 04:00:03 PDT
