I have invastigated a bit more the problem. I'm still using GCC4.4.3 on
a fedora core 12 workstation. I have reinstalled GCC4 and the standard
C/C++/fortran libraries. The AmberTools 1.3 have been compiled as following:
configure_at -nosleap gcc
make -f Makefile_at
Then I went to the test directory and modify Makefile_at file to skip
the nab test. The test failed at:
load and saveamberparm: 94 ff
When I check the log, the failure happens when loading the nucleic acids:
>> parm94 = loadamberparams parm94.dat
Loading parameters: /home/software/amber11/dat/leap/parm/parm94.dat
Reading title:
PARM94 for DNA, RNA and proteins with TIP3P Water. USE SCEE=1.2 in
energy progs
(UNKNOWN ATOM TYPE: IM)
(UNKNOWN ATOM TYPE: Li)
(UNKNOWN ATOM TYPE: IP)
(UNKNOWN ATOM TYPE: K)
(UNKNOWN ATOM TYPE: Rb)
(UNKNOWN ATOM TYPE: Cs)
(UNKNOWN ATOM TYPE: IB)
(UNKNOWN ATOM TYPE: EP)
>> #
>> # Load DNA/RNA libraries
>> #
>> loadOff all_nucleic94.lib
Loading library: /home/software/amber11/dat/leap/lib/all_nucleic94.lib
Loading: DA
At that point, I don't see what to do. My feeling is that the problem is
related to a weird configuration of GCC4.4.3 and or the C/C++ libraries.
I don't know if it's specific to fedora core 12, GCC4.4.3 or if I did
something really wrong during the install. I think I will reinstall
again my machine, but with another linux this time. Maybe CentOS?
Regards,
Nicolas
Nicolas Sapay a écrit :
> case a écrit :
>> On Thu, Feb 18, 2010, Nicolas Sapay wrote:
>>
>>
>>> Running test to make dna duplex:
>>> Can't open residue library
>>> /home/software/amber11/dat/reslib/al_nucleic94.liib.
>>>
>> ^^^^^^^^^^^^^^^^^^^^^
>>
>> This is most odd, but I'm suspecting a copy/paste error in your report?
>> The file should be "all_nucleic94.lib"; if it is really called
>> what you post, it's hard to tell where that is coming from. Try looking
>> for "nucleic94" in amber11/src/nab/wc_helix.nab; can you find out where
>> the "liib" is coming from?
>>
>> ...dac
>>
> There is not copy paste error. The error message is really:
>
> /home/software/amber11/dat/reslib/al_nucleic94.liib
>
> The weird thing is that "al_nucleic94.liib is mentionned nowhere in
> the any file of the amber11/src/nab/ directory.
>
> Nicolas
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Received on Thu Feb 18 2010 - 09:00:02 PST
