Help on align.top

6 Jul 2004


      Dear all,
I just did a modelling based on a model(1L9H).
My align2d.top is :
protein:~/syliu>more align2d.top
INCLUDE
READ_MODEL FILE = '1L9H'
SEQUENCE_TO_ALI ALIGN_CODES = '1L9H'
READ_ALIGNMENT FILE = 'tget.ali', ALIGN_CODES = ALIGN_CODES 'tget', 
ADD_SEQUENCE = on
ALIGN2D
WRITE_ALIGNMENT FILE='tget-1L9H.ali', ALIGNMENT_FORMAT = 'PIR'
WRITE_ALIGNMENT FILE='tget-1L9H.pap', ALIGNMENT_FORMAT = 'PAP'
My target sequence is :
protein:~/syliu>more tget.ali
>P1;tget
sequence:tget:::::::0.00: 0.00
MNTSAPPAVSPNITVLAPGKGPWQVAFIGITTGLLSLATVTGNLLVLISFKVNTELKTVNNYFLLSLACADLIIGTFSMNLYTTYLLMGHWALGTLACDLWLAL
DYVASNASVMNLLLISFDRYFSVTRPLSYRAKRTPRRAALMIGLAWLVSFVLWAPAILFWQYLVGERTVLAGQCYIQFLSQPIITFGTAMAAFYLPVTVMCTLY
WRIYRETENRARELAALQGSETPGKGGGSSSSSERSQPGAEGSPETPPGRCCRCCRAPRLLQAYSWKEEEEEDEGSMESLTSSEGEEPGSEVVIKMPMVDPEAQ
APTKQPPRSSPNTVKRPTKKGRDRAGKGQKPRGKEQLAKRKTFSLVKEKKAARTLSAILLAFILTWTPYNIMVLVSTFCKDCVPETLWELGYWLCYVNSTINPM
CYALCNKAFRDTFRLLLLCRWDKRRWRKIPKRPGSVHRTPSRQC*
When I do mod align2d.top , the modeller ends successfully and output a 
"STOP". But I got a log:
MODELLER 6v2, 17 Feb 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 protein 2.4.18-14 i686
Date and time of compilation         : 07/16/2002 11:42:16
Job starting time (YY/MM/DD HH:MM:SS): 2004/07/06  23:22:21.841
dispers_247E> Internal error:      641      642
recover____E> ERROR_STATUS >= STOP_ON_ERROR:        1       1
Dynamically allocated memory at          finish [B,kB,MB]:     25421225   
24825.414    24.244
Starting time                                            : 2004/07/06  
23:22:21.841
Closing time                                             : 2004/07/06  
23:37:12.289
Total CPU time [seconds]                                 :     832.85
So, what is the problem on the error information ? (dispers_247E> Internal 
error:      641      642)?
Shiyong Liu

Liu Shiyong

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