AMBER Archive (2009)

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

From: Alan (alanwilter_at_gmail.com)
Date: Tue Sep 22 2009 - 16:41:18 CDT

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_at_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_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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