Hi Modellers,
I am having a problem with the 'sequence_search' command
in Modeller6, Modeller crashes after ~5 hours of searching
with the following message (which is always the same, and
looks similar to the one Francesco Musiani reported yesterday):
projekte/limpo> mod6v1 search.top
/home/thorsten/modeller6v1/bin/mod6v1: line 41: 1774 Killed $NICE ${EXECUTABLE} $STEERF
>$LOGF
I have already replaced the CHAINS files with the files from
the new distribution, so the 1xnb-error does not occur anymore.
As advised, I checked the stacksize, it is set to unlimited
in the .cshrc-file, and remains set to this value before and
after modeller's crash. I also tried different sequence-files,
but there was no effect.
Modeller is running on a Pentium3-800, SUSE-Linux 7.1, 640 MB RAM.
Can anyone tell me what this error message means and
how to solve this problem?
Thanks in advance!
Thorsten Schweikardt
Molecular Biophysics
University of Mainz
Germany
My files:
search.top:
-----------
SET OUTPUT_CONTROL = 1 1 1 1 0
SET FILE = 'limpo.pir'
SEQUENCE_SEARCH ALIGN_CODES = 'limpo', DATA_FILE = ON
limpo.pir:
----------
>P1;limpo
sequence:limpo:::::::0.00:0.00
TLHDKQIRICHLFEQLSSATVIGDGDKHKHSDRLKNVGKLQPGAIFSCFHPDHLEEARHL
YEVFWEAGDFNDFIEIAKEARTFVNEGLFAFAAEVAVLHRDDCKGLYVPPVQEIFPDKFI
PSAAINEAFKKAHVRPEFDESPILVDVQDTGNILDPEYRLAYYREDVGINAHHWHWHLVY
PSTWNPKYFGKKKDRKGELFYYMHQQMCARYDCERLSNGMHRMLPFNNFDEPLAGYAPHL
THVASGKYYSPRPDGLKLRDLGDIEISEMVRMRERILDSIHLGYVISEDGSHKTLDELHG
TDILGALVESSYESVNHEYYGNLHNWGHVTMARIHDPDGRFHEEPGVMSDTSTSLRDPIF
YNWHRFIDNIFHEYKNTLKPYDHDVLNFPDIQVQDVTLHARVDNVVHTFMREQELELKHG
INPGNARSIKARYYHLDHEPFSYAVNVQNNSASDKHATVRIFLAPKYDELGNEIKADELR
RTAIELDKFKTDLHPGKNTVVRHSLDSSVTLSHQPTFEDLLHGVGLNEHKSEYCSCGWPS
HLLVPKGNIKGMEYHLFVMLTDWDKDKVDGSESVACVDAVSYCGARDHKYPDKKPMGFPF
DRPIHTEHISDFLTNNMFIKDIKIKFHE*
logfile:
--------
MODELLER 6v1, 17 Jan 2002
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2002 Andrej Sali
All Rights Reserved
Written by A. Sali
with help from A. Fiser, R. Sanchez, M.A. Marti-Renom,
B. Jerkovic, A. Badretdinov, F. Melo,
J.P. Overington & E. Feyfant
Rockefeller University, New York, USA
Harvard University, Cambridge, USA
Imperial Cancer Research Fund, London, UK
Birkbeck College, University of London, London, UK
Kind, OS, HostName, Kernel, Processor: 4, Linux at2 2.4.0-4GB i686
Date and time of compilation : 01/24/2002 16:28:15
Job starting time (YY/MM/DD HH:MM:SS): 2002/03/01 11:51:45.460
TOP_________> 2 2 SET FILE = 'limpo.pir'
TOP_________> 3 3 SEQUENCE_SEARCH ALIGN_CODES = 'limpo', DATA_FILE = ON
openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v1}/modlib//CHAINS_3.0_40_XN.cod
openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v1}/modlib//CHAINS_3.0_40_XN.cod
openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v1}/modlib//CHAINS_all.seq
openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v1}/modlib//CHAINS_all.seq
openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v1}/modlib//as1.sim.mat
rdrrwgh_268_> Number of residue types: 20
openf5__224_> Open 11 OLD SEQUENTIAL limpo.pir
seqsearc_> 1 limpo 1xnb 628 185 104 16.56 56.22 135506.30
_aln.pos 10 20 30 40 50 60
limpo TLHDKQIRICHLFEQLSSATVIGDGDKHKHSDRLKNVGKLQPGAIFSCFHPDHLEEARHLYEVFWEAG
1xnb ASTD-------YW-Q--NWT---DG------------G----G-I-----------------V-----
_consrvd * * * ** * * * *
_aln.p 70 80 90 100 110 120 130
limpo DFNDFIEIAKEARTFVNEGLFAFAAEVAVLHRDDCKGLYVPPVQEIFPDKFIPSAAINEAFKKAHVRP
1xnb --N-----A------VN-G--S-G------------GNY--------------S--VN--W-------
_consrvd * * ** * * * * *
_aln.pos 140 150 160 170 180 190 200
limpo EFDESPILVDVQDTGNILDPEYRLAYYREDVGINAHHWHWHLVYPSTWNPKYFGKKKDRKGELFYYMH
1xnb ----S-------NTGN-----F-V------VG-KG--W-------TTGSP--F-----RT--I-NY-N
_consrvd * *** ** * * * * * *
_aln.pos 210 220 230 240 250 260 270
limpo QQMCARYDCERLSNGMHRMLPFNNFDEPLAGYAPHLTHVASGKYYSPRPDGLKLRDLGDIEISEMVRM
1xnb ----A---------GV--WAP-NG-N----GY---LT-L----Y------GWT-R-------SPLI--
_consrvd * * * * ** ** * * * *
[....]
The alignments stop with 1hv8.pdb, before the summary of the 1hv8-alignment
is written.
