Re: Problem with SEQUENCE_SEARCH

[Alex Brown <>]

I don't know if it would work, but you could remove the INCLUDE command 
from line 1 of your script. It doesn't appear to be nessessary.

If you think 2 hours running time is long, it took just over 6 hours on 
my setup (same search). Try running overnight. Setting the 
OUTPUT_CONTROL variable to 'all-on' may also increase the execution time 
and may even affect the memory usage.

Cheers,

Alex

On Monday, September 23, 2002, at 10:13  pm, Juan Palacios wrote:

> My .top file is:
> --------------------------------------------------------------------------------------------------------------
> INCLUDE
>  
> SET OUTPUT_CONTROL = 1 1 1 1 1
> SET SEARCH_RANDOMIZATIONS = 3
> SET FILE = 'TvLDH.ali'
> SEQUENCE_SEARCH ALIGN_CODES = 'TvLDH', DATA_FILE  = ON
> -----------------------------------------------------------------------------------------------------------------
>  
> the log file is:
>  
> ----------------------------------------------------------------------------------------------------------------
> 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 bioinf4 2.4.4-4GB i686
> Date and time of compilation         : 05/24/2002 09:27:23
> Job starting time (YY/MM/DD HH:MM:SS): 2002/09/23  15:16:01.528
>  
> TOP_________>   105  705 SET SEARCH_RANDOMIZATIONS = 3
>  
> TOP_________>   106  706 SET FILE = 'TvLDH.ali'
>  
> TOP_________>   107  707 SEQUENCE_SEARCH ALIGN_CODES = 'TvLDH', 
> DATA_FILE  = ON
>  
> openf5__224_> Open       11  OLD  SEQUENTIAL  
> ${MODINSTALL6v2}/modlib//CHAINS_3.0_40_XN.cod
>  
> Dynamically allocated memory at         amaxchn [B,kB,MB]:      
> 2306323    2252.269     2.199
> openf5__224_> Open       11  OLD  SEQUENTIAL  
> ${MODINSTALL6v2}/modlib//CHAINS_3.0_40_XN.cod
> openf5__224_> Open       11  OLD  SEQUENTIAL  
> ${MODINSTALL6v2}/modlib//CHAINS_all.seq
>  
> Dynamically allocated memory at         amresdb [B,kB,MB]:      
> 5689471    5556.124     5.426
> openf5__224_> Open       11  OLD  SEQUENTIAL  
> ${MODINSTALL6v2}/modlib//CHAINS_all.seq
>  
> Dynamically allocated memory at         amaxseq [B,kB,MB]:      
> 5877209    5739.462     5.605
>  
> Dynamically allocated memory at         amaxbnd [B,kB,MB]:    
> 110299725  107714.600   105.190
> openf5__224_> Open       11  OLD  SEQUENTIAL  
> ${MODINSTALL6v2}/modlib//as1.sim.mat
> rdrrwgh_268_> Number of residue types:       20
> openf5__224_> Open       11  OLD  SEQUENTIAL  TvLDH.ali
>  
> ---------------------------------------------------------------------------------------------------------------------------------------------------------------
>  
>  
>  
> After 2 hours of executing delivery the following mistake
> The error is:
>  
> /usr/local/modeller6v2/bin/mod6v2 : line38 : 2030  terminated         
> $NICE ${EXECUTABLE}  $STEERF  >$LOGF
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> WHAT IS A PROBLEM???
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