Hello,
I had to reinstall my system (Fedora core 12 - 64 bits) and since then,
I have much difficulties to make the AmberTools work again. Each time I
source a leaprc, xleap crashes due to a segmentation fault:
source /home/software/amber10/dat/leap/cmd/leaprc.ff99SB
xleap < leap.in
-I: Adding /home/software/amber10/dat/leap/prep to search path.
-I: Adding /home/software/amber10/dat/leap/lib to search path.
-I: Adding /home/software/amber10/dat/leap/parm to search path.
-I: Adding /home/software/amber10/dat/leap/cmd to search path.
/home/software/amber10/exe/xleap: line 19: 1928 segmentation fault
(core dumped) $AMBERHOME/bin/xaLeap -I$AMBERHOME/dat/leap/prep
-I$AMBERHOME/dat/leap/lib -I$AMBERHOME/dat/leap/parm
-I$AMBERHOME/dat/leap/cmd $*
The last lines of the log file are:
Loading parameters: /home/software/amber10/dat/leap/parm/frcmod.ff99SB
Reading force field modification type file (frcmod)
Reading title:
Modification/update of parm99.dat (Hornak & Simmerling)
>> #
>> # Load DNA/RNA libraries
>> #
>> loadOff all_nucleic94.lib
Loading library: /home/software/amber10/dat/leap/lib/all_nucleic94.lib
Loading: DA
Only GAFF seems to be OK. Note that I have recompiled Amber10 and
AmberTools1.2 with GCC4. I tried to test the AmberTools install unsing:
make -f Makefile_at test
Unfortunately, the test lamentably crashes at the first attempt:
make[1]: entering directory "/home/software/amber10/test/nab"
=====================================================
Running test to make dna duplex:
Can't open residue library
/home/software/amber11/dat/reslib/al_nucleic94.liib.
make[1]: *** [duplex_test] Error 1
make[1]: living directory "/home/software/amber10/test/nab "
make: *** [test.nab] Erreur 2
At that point, any suggestion is welcomed.
Regards,
Nicolas
ps: I also tried version 1.3 with the same result.
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Received on Thu Feb 18 2010 - 06:00:04 PST
