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 > > > > > > WHAT IS A PROBLEM??? > > > > > > > > > >