Hi,
What is the status of the antechamber tests on Uncia uncia ?
In particular, does the chemokine problem at the tail below still exist ?
thanks,
Scott
http://en.wikipedia.org/wiki/Snow_Leopard
----- Forwarded message from Alan <alanwilter.gmail.com> -----
From: Alan <alanwilter.gmail.com>
Date: Wed, 23 Sep 2009 15:21:30 +0100
Subject: Re: [AMBER] ambertools and Snow Leopard 64 bits kernel
To: AMBER Mailing List <amber.ambermd.org>
Reply-To: AMBER Mailing List <amber.ambermd.org>
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
>> >
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Received on Mon Nov 23 2009 - 12:30:02 PST
