Dears:
When I run below program, it will be crash.
INCLUDE SET OUTPUT_CONTROL = 1 1 1 1 1 SET ATOM_FILES_DIRECTORY = '/usr/local/lib/pdb' SET OUTPUT = 'SHORT' # 'LONG' SET SIGNIF_CUTOFF = 8 3 SET SEARCH_RANDOMIZATIONS = 10 SET STOP_ON_ERROR = 2 CALL ROUTINE = 'sequence_srch', SEGFILE = 'ny10.chn', SEQUENCE = 'ny10'
I want to use this program to get the alignment and using the alignment to get the template sequence and get the model by homology modelling. The ny10.chn is one chain protein with 68 a.a. , and I set the ATOM_FILES_DIRECTORY is the all PDB files in my server. This program will be crash after abour the 45 min. I don't know what's wrong. My server is RedHat Linux 7.1 with PIII 1G cpu and 512Mb ram.
Your friendly, Jack Wang
At 03:38 PM 11/14/01 +0800, Tsu-Sheng Wang wrote: >Dears: > > When I run below program, it will be crash. > >INCLUDE >SET OUTPUT_CONTROL = 1 1 1 1 1 >SET ATOM_FILES_DIRECTORY = '/usr/local/lib/pdb' >SET OUTPUT = 'SHORT' # 'LONG' >SET SIGNIF_CUTOFF = 8 3 >SET SEARCH_RANDOMIZATIONS = 10 >SET STOP_ON_ERROR = 2 >CALL ROUTINE = 'sequence_srch', SEGFILE = 'ny10.chn', SEQUENCE = 'ny10' > > I want to use this program to get the alignment and using the alignment >to get the template sequence and get the model by homology modelling. > The ny10.chn is one chain protein with 68 a.a. , and I set the >ATOM_FILES_DIRECTORY is the all PDB files in my server. This program will >be crash after abour the 45 min. I don't know what's wrong. My server is >RedHat Linux 7.1 with PIII 1G cpu and 512Mb ram.
7.1 is notorious for its bugs. It crashes randomly blastpgp jobs too at certain conditions. I would advise you to reproduce it on 6.2.
>Your friendly, >Jack Wang > >
-- Azat Badretdinov, Accelrys
if still a problem, would you please try it with the pre-release of modeller 6 (ask bozidar@rockefeller.edu). if still a problem, would you please email us the input files.
thanks, andrej
-----Original Message----- From: owner-modeller_usage@salilab.org [mailto:owner-modeller_usage@salilab.org]On Behalf Of Azat Badretdinov Sent: Wednesday, November 14, 2001 9:56 AM To: Tsu-Sheng Wang Cc: modeller_usage@salilab.org Subject: Re: Crash in running the SEQUENCE_SRCH
At 03:38 PM 11/14/01 +0800, Tsu-Sheng Wang wrote: >Dears: > > When I run below program, it will be crash. > >INCLUDE >SET OUTPUT_CONTROL = 1 1 1 1 1 >SET ATOM_FILES_DIRECTORY = '/usr/local/lib/pdb' >SET OUTPUT = 'SHORT' # 'LONG' >SET SIGNIF_CUTOFF = 8 3 >SET SEARCH_RANDOMIZATIONS = 10 >SET STOP_ON_ERROR = 2 >CALL ROUTINE = 'sequence_srch', SEGFILE = 'ny10.chn', SEQUENCE = 'ny10' > > I want to use this program to get the alignment and using the alignment >to get the template sequence and get the model by homology modelling. > The ny10.chn is one chain protein with 68 a.a. , and I set the >ATOM_FILES_DIRECTORY is the all PDB files in my server. This program will >be crash after abour the 45 min. I don't know what's wrong. My server is >RedHat Linux 7.1 with PIII 1G cpu and 512Mb ram.
7.1 is notorious for its bugs. It crashes randomly blastpgp jobs too at certain conditions. I would advise you to reproduce it on 6.2.
>Your friendly, >Jack Wang > >
-- Azat Badretdinov, Accelrys
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Andrej Sali -
Azat Badretdinov -
Tsu-Sheng Wang