Jorge,
Sorry I might have confused your setup ...... I meant AMBER 11, Amber
Tools 1.5, gcc 4.5.1, opensuse 11.4 ...
Vlad
On 05/25/2011 09:11 PM, JORGE IULEK wrote:
> Thanks, Vlad, for your comments.
>
>> I don't think "al_nucleic94.liib" is a valid file name.
> As a matter of fact.
>
>> if you search for it in some makefile and replace the "ii" with "i", do
>> you mange to do the tests ?
> I searched, but did not find anywhere a double i.
>
>> I compiled and tested myself with exactly same environment as yours and
>> did not notice any problems
> Just to check, you manage to get with AmberTools 1.3 and Amber10,
> bugfixes applied, openSuSE 11.4 64 -bits, kernel 2.6.37.6-0.5-default, gcc
> 4.5-19.1 ? The Amber and Ambertools packages you have are the same?
>
> J.
>
>> Vlad
>>
>> On 05/25/2011 03:46 PM, JORGE IULEK wrote:
>>> Dear amber friends,
>>>
>>> I recently noved to a new laptop (where I calculate energies after
>>> cluster productive runs). In my former laptop, I had openSuSE 11.2 (64
>>> bits), to which I compiled AmberTools 1.3 and Amber10, gcc version 4.4(.1
> as
>>> reported by configure)-4.2, all patches applied, following instructions
> at
>>> http://archive.ambermd.org/201001/0150.html, and things ran as expected.
> To
>>> my new laptop, I went to openSuSE 11.4 (64 bits), gcc is 4.5(.1 as
> reported
>>> by configure)-19.1 (as reported by yast2). AmberTools compilation seems
> to
>>> go fine, but at "test" I get the error:
>>>
>>> "
>>> make[1]: Entering directory `/usr/local/amber11/test/nab'
>>> =====================================================
>>> Running test to make dna duplex:
>>>
>>> Can't open residue library
> /usr/local/amber11/dat/reslib/al_nucleic94.liib.
>>> make[1]: *** [duplex_test] Error 1
>>> make[1]: Leaving directory `/usr/local/amber11/test/nab'
>>> make: *** [test.nab] Error 2
>>> "
>>>
>>> Exactly as pasted, "al_nucleic94.liib".
>>>
>>> The closest I found to this was
>>> http://archive.ambermd.org/201002/0267.html.
>>>
>>> I tried a number of alternatives. One of them, the intel compiler,
> did
>>> not compile (unfortunately this OS is said not to be supported for it,
>>> although I followed the instructions at
>>>
> http://software.intel.com/en-us/articles/installing-intel-compilers-on-opensuse/for
>>> former versions, but without success (to compile amber, not compiler
>>> installation).
>>>
>>> I think the best I could do for while was to put openSuSE 11.2 in a
>>> virtual machine, there it compiled nicely (as in the old laptop) and it
>>> seems to work, although during a calculation I had a problem on " SA
> Bomb
>>> in sa_arc(): Allocation aborted 0 0 0
>>> 0 5014" for a frame (memory limits in the virtual
>>> machine?). But it does not seem to be a good idea to run amber under a
>>> virtual machine. I made a (senseless?) test, simply copied the amber10
> and
>>> amber11 directories from the VM to the host OS, (hand) made the
>>> (non-transferable) links and mk_crd_hg and sander seem to work (yes, they
>>> could even calculate energias), but not tleap (so prm files have to come
>>> from elsewhere). In fact, for this transferred tleap I get:
>>>
>>> "
>>> $AMBERHOME/bin/teLeap -I$AMBERHOME/dat/leap/prep
> -I$AMBERHOME/dat/leap/lib
>>> -I$AMBERHOME/dat/leap/parm -I$AMBERHOME/dat/leap/cmd -s -f leaprc.ff99SB
> -f
>>> leap.inp
>>> -I: Adding /usr/local/amber11/dat/leap/prep to search path.
>>> -I: Adding /usr/local/amber11/dat/leap/lib to search path.
>>> -I: Adding /usr/local/amber11/dat/leap/parm to search path.
>>> -I: Adding /usr/local/amber11/dat/leap/cmd to search path.
>>> -s: Ignoring startup file: leaprc
>>> -f: Source leaprc.ff99SB.
>>> -f: Source leap.inp.
>>>
>>> Welcome to LEaP!
>>> Sourcing: /usr/local/amber11/dat/leap/cmd/leaprc.ff99SB
>>> Log file: ./leap.log
>>> Loading parameters: /usr/local/amber11/dat/leap/parm/parm99.dat
>>> Reading title:
>>> PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP
>>> incl.02/04/99
>>> Loading parameters: /usr/local/amber11/dat/leap/parm/frcmod.ff99SB
>>> Reading force field modification type file (frcmod)
>>> Reading title:
>>> Modification/update of parm99.dat (Hornak& Simmerling)
>>> Loading library: /usr/local/amber11/dat/leap/lib/all_nucleic94.lib
>>> Segmentation fault
>>> "
>>>
>>> So again I understand the the problem is the all_nucleic94.lib file
>>> (which is in there, in the due place, but...).
>>>
>>> Some points: i) I would very prefer to use ambertools 1.3 and
> amber10
>>> now yet the results are to be compared to several others runs with those
>>> program versions; ii) I would prefer to keep the most updated version of
>>> openSuSE.
>>> Anyway, I think relating these problems might help development.
> Anyway
>>> to overcome the error and compile natively under my (most uptodate)
>>> distribution.
>>> Suggestions?
>>>
>>> Thanks,
>>>
>>> Jorge
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Dr. Vlad Cojocaru
Max Planck Institute for Molecular Biomedicine
Department of Cellular and Developmental Biology
Roentgenstrasse 20
48149 Muenster, Germany
tel: +49-251-70365-324
fax: +49-251-70365-399
email: vlad.cojocaru[at]mpi-muenster.mpg.de
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Received on Wed May 25 2011 - 14:00:04 PDT
