In Linux 64 bits I didn't have problems.
But I DO NEED ambertools (specially antechamber) in Mac running kernel 64 bits.
>From what I see of the case that failed for antechamber (1b2t), in
Run.1b2t file:
# Do NOT use antechamber to assign atom types for your proteins! This test
# just demonstrates antechamber can handle pretty large molecules now
I think I can live with antechamber since I use just for small molecules.
But I would love to see this problem solved.
Alan
On Wed, Sep 23, 2009 at 03:18, <gilbert.bluemarble.net> wrote:
> I don't know how you have modified your makefile but I found (when compiling
> some 32 bit code on a 64 bit linux system) that I needed -m32 on both the
> compile and linker lines (CFLAGS, FFLAGS and LDFLAGS all had the -m32 option).
> That may be of help trying to compile 64 bit code on a 32 bit OS. But I have
> compiled ambertools on my 64 bit linux machine with nothing other that the
> standard configure and make.
>
> Kevin Gilbert
> Serena Software
>
> Quoting Tom Joseph <ttjoseph.gmail.com>:
>
>> I was able to reproduce these failures.
>>
>> In the nab testcase, strange object code that nukes pointers returned
>> from functions is generated, causing the segfault. I suspect it has
>> something to do with 32 vs 64 bit linking, but I don't know enough
>> about Apple's linker to know what's going on here. For the antechamber
>> failure...not sure what's going on there; perhaps some antechamber
>> expert can comment?
>>
>> For the time being perhaps it's best to use nab and antechamber on
>> another platform.
>>
>> --Tom
>>
>> 2009/9/22 Alan <alanwilter.gmail.com>:
>> > Thanks Tom, it did help.
>> >
>> > However, nab still fails and from antechamber the last test failed with:
>> > ==============================================================
>> > cd antechamber/chemokine && ./Run.1b2t
>> > make: *** [test.antechamber] Error 1
>> >
>> > [DETAILED]
>> >
>> > ../../../exe/antechamber -fi pdb -fo ac -i 1b2t.pdb -o 1b2t.ac -at amber \
>> >> -s 2 -pf yes
>> >
>> > The atom number exceeds the MAXATOM, reallocate memory
>> > Info: the bond number exceeds MAXBOND, reallocate memory automatically
>> > Running: /Users/alan/Programmes/amber10/bin/bondtype -j full -i
>> > ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
>> >
>> > Info: the atom number exceeds the MAXATOM, reallocate memory automatically
>> > ---Judge bond type for Residue 1 with ID of 0 and Name of MET ---
>> >
>> > [snip]
>> >
>> > ---Judge bond type for Residue 15 with ID of 14 and Name of LYS ---
>> >
>> > The frozen atom type can only be 1, 2, 3, 7 (aromatic single), 8
>> > (aromatic double)Error: cannot run
>> > "/Users/alan/Programmes/amber10/bin/bondtype -j full -i
>> > ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in
>> > judgebondtype() of antechamber.c properly, exit
>> >
>> > Many thanks,
>> >
>> > Alan
>> >
>> > On Tue, Sep 22, 2009 at 19:12, Tom Joseph <ttjoseph.gmail.com> wrote:
>> >> 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.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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Received on Wed Sep 23 2009 - 07:30:02 PDT
