AMBER Archive (2009)

Subject: Re: [AMBER] ambertools and Snow Leopard 64 bits kernel

From: Tom Joseph (ttjoseph_at_gmail.com)
Date: Tue Sep 22 2009 - 13:12:55 CDT

When you compiled antechamber, did you get warnings such as the following?

alc.c:155: warning: call to __builtin___strcpy_chk will always
overflow destination buffer

If so, this is a bug in antechamber - there are several instances
where a string is copied into a char array that is too small. Please
try the attached patch.

--Tom

2009/9/22 Alan <alanwilter_at_gmail.com>:
> Hi there,
>
> I would like to know if there's other already using (or trying to use)
> AmberTools with Snow Leopard in 64 bits kernel.
>
> I did a try and although I had a nice compilation (gcc/gfortran with
> -m64), running tests failed for:
>
> nab, antechamber (some cases)
>
> For example:
>
> make -f Makefile_at test.nab
> ( cd nab; make test )
> =====================================================
> Running test to make dna duplex:
>
> /bin/sh: line 1: 21844 Segmentation fault      ./duplex < duplex.in
> make[1]: *** [duplex_test] Error 139
> make: *** [test.nab] Error 2
>
> make -f Makefile_at test.antechamber
> cd antechamber/top2mol2 && ./Run.top2mol2
> diffing sustiva.mol2.save with sustiva.mol2
> PASSED
> ==============================================================
> [snip]
> ==============================================================
> diffing fluorescein_f2.mol2.save with fluorescein_f2.mol2
> possible FAILURE:  check fluorescein_f2.mol2.dif
> ==============================================================
> cd antechamber/c60 && ./Run.c60
> Abort
>  ./Run.c60:  Program error
> make: *** [test.antechamber] Error 1
>
> Many thanks in advance,
>
> Alan
>
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>



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