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.
Hi,
It's really hard to guess what's happening without looking at detailed .log file, .top file, etc. If you could post those at the list it would be helpful.
Thanks, Bozidar
-----Original Message----- From: owner-modeller_usage@salilab.org [mailto:owner-modeller_usage@salilab.org] On Behalf Of Thorsten Schweikardt Sent: Friday, March 01, 2002 10:54 AM To: modeller_usage@salilab.org Subject: Problem with Sequence_Search
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.
Hi,
It would be informative to take a look at long .log output and .top file. What executable are you running?
Thanks, Bozidar
-----Original Message----- From: owner-modeller_usage@salilab.org [mailto:owner-modeller_usage@salilab.org] On Behalf Of Thorsten Schweikardt Sent: Friday, March 01, 2002 10:54 AM To: modeller_usage@salilab.org Subject: Problem with Sequence_Search
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.
participants (2)
-
Bozidar Jerkovic -
Thorsten Schweikardt