AMBER Archive (2009)

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

From: Scott Brozell (sbrozell_at_rci.rutgers.edu)
Date: Wed Dec 09 2009 - 15:48:30 CST

Hi,

Fixed in the upcoming AmberTools 1.3 release.
Thanks for the report.
Scott

On Wed, Sep 23, 2009 at 03:21:30PM +0100, Alan wrote:
> 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
>
> > Quoting Tom Joseph <ttjoseph_at_gmail.com>:
> >
> >> 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_at_gmail.com>:
> >> >
> >> > 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]
> >> >>
> >> >> 2009/9/22 Alan <alanwilter_at_gmail.com>:
> >> >>>
> >> >>> 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

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