I don't think "al_nucleic94.liib" is a valid file name.
if you search for it in some makefile and replace the "ii" with "i", do
you mange to do the tests ?
I compiled and tested myself with exactly same environment as yours and
did not notice any problems
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
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>
--
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 - 07:30:05 PDT
