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Re: FW: Modeller6v2 trouble



... and maybe also you have to specify the numeration of the residues in the
alignment file

>P1;1cii
structureX:1cii
like
>P1;1cii
structureX:1cii:start::end:::::

and check if you have chain in the pdb...

Hope it helps

(and also the war will end soon)

Luca

--------------------------------------------------------
Luca Settimo, Ph.D. Student


Molecular Structures and Biocomputing
Department of Biochemistry and Pharmacy
Åbo Akademi University
Tykistökatu 6A
20520 Turku Finland
phone: +358-2-215-4600
fax: +358-2-2153280
">mailto:
Webpage URL http://www.abo.fi/~lsettimo
--------------------------------------------------------






Modeller Care wrote:

> ------ Forwarded Message
> From: Mario Garcia <>
> Date: Fri, 21 Mar 2003 16:53:17 +0100 (CET)
> To: 
> Subject: Modeller6v2 trouble
>
> Dear Dr. Bozidar,
> I have some error after a modeling jot execution (mod script.top) in
> Modeller6v2 under an IRIX 6.2 box. Bellow, I include the corresponding
> .top and .ali input files and the resulting .log file. Could you give some
> hints to help me? Thank you very much in advance for your help.
> Regards,
>     Mario Garcia.
>
> -------------------------------------------------------------------------
>    Mario Garcia de Lacoba, PhD.       Phone   : +341 915611800 (ext.4334)
>                                       Fax     : +341 915627518
> Centro de Investigaciones Biologicas  E-mail  : 
>               C.S.I.C.
>           c/ Velazquez, 144
>          28006-Madrid. SPAIN.
> -------------------------------------------------------------------------
>
> ======================MOB3.top===================================
> # Homology modelling by the MODELLER TOP routine 'model'.
>
> INCLUDE                             # Include the predefined TOP routines
>
> SET OUTPUT_CONTROL = 1 1 1 1 1      # uncomment to produce a large log file
> SET ALNFILE  = 'MOB4.ali'      # alignment filename
> SET KNOWNS   = '1cii'               # codes of the templates
> SET SEQUENCE = '1mob'               # code of the target
> SET ATOM_FILES_DIRECTORY = './:../atom_files' # directories for input atom
> files
> SET STARTING_MODEL= 1               # index of the first model
> SET ENDING_MODEL  = 1               # index of the last model
>                                     # (determines how many models to
> calculate)
> CHECK_ALIGNMENT
> CALL ROUTINE = 'model'              # do homology modelling
>
> ================MOB4.ali================================
> C; mob_1cii.phy align
> >P1;1cii
> structureX:1cii
> EIMAVDIYVNPPRVDVFHGTPPAWSSFGNKTIWGGNEWVDDSPTRSDIEK
> RDKEITAYKNTLSAQQKENENKRTEAGKRLSAAIAAREKDENTLKTLRAG
> NADAADITRQEFRLLQAELREYGFRTEIAGYDALRLHTESRMLFADADSL
> RISPREARSLIEQAEKRQKDAQNADKKAADMLAEYERRKGILDTRLSELE
> KNGGAALAVLDAQQARLLGQQTRNDRAISEARNKLSSVTESLNTARNALT
> RAEQQLTQQKNTPDGKTIVSPEKFPGRSSTNDSIVVSGDPRFAGTIKITT
> SAVIDNRANLNYLLSHSGLDYKRNILNDRNPVVTEDVEGDKKIYNAEVAE
> WDKLRQRLLDARNKITSAESAVNSARNNLSARTNEQKHANDALNALLKEK
> ENIRNQLSGINQKIAEEKRKQDELKATKDAINFTTEFLKSVSEKYGAKAE
> QLAREMAGQAKGKKIRNVE-EALKTYEKYRADINKKINAKDRAAIAAALE
> SVKLSDISSNLNRFSRGLGYAGKFTSLADWITEFGKAVRTENWRPLFVKT
> ETIIAGNAATALVALVFSILTGSALGIIGYGLLMAVTGALIDESLVEKAN
> KFW*
> >P1;1mob
> sequence:1mob
> ------MSYMVARMQKMKAGNLGGAFKHNERVFETHSNKDINPSRSHLN-
> --YELTDRDRSVSYEKQIKDYVNENKVSNRAIRKDAVLCDEWIITSDKD-
> -----------FFEKLDEEQTRTFFETAKNYFAENYG-ESNIAYASVHLD
> ESTPHMHMGVVPFENGKLSSKAMFDREELKHIQEDLPR--YMSDHGFELE
> -------------------------------RGKLNSEAKHKTVAEFKRA
> MADMELKEELLEKYHAPLFVDERTG--ELNNDTEAFWHEKEFADMFEVQS
> PIRETTNQEKMDWLRKQYQEELKKLESSKKP-LEDDLSHLEELLDKKTKE
> YIKIDSEASERASELSKAEGYINTLEN--HSKSLEAKIECLESDNLQLEK
> Q----KATKLEAKALNES----ELRELKPKKNFLGKEHYELSPEQ---FE
> GLKAEVYRSRTLLHHKDIELEQAKRQVSLRASKNYFTASLERAKEKAKGE
> SIDR--LKSEIKRLKN------------E----N-SILRQQNDK-MLGKL
> RELMPDKAFKNLLSELKAIKP-----------IVNIIKKAIEKSLF----
> ---*
>
> =====================MOB4.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, IRIX64 akilonia 6.5 IP30
> Date and time of compilation         : 07/05/2002 17:12:26
> Job starting time (YY/MM/DD HH:MM:SS): 2003/03/21  23:47:53.033
>
> TOP_________>   105  705 SET ALNFILE  = 'MOB4.ali'
>
> TOP_________>   106  706 SET KNOWNS   = '1cii'
>
> TOP_________>   107  707 SET SEQUENCE = '1mob'
>
> TOP_________>   108  708 SET ATOM_FILES_DIRECTORY = './:../atom_files'
>
> TOP_________>   109  709 SET STARTING_MODEL = 1
>
> TOP_________>   110  710 SET ENDING_MODEL  = 1
>
> TOP_________>   111  711 CHECK_ALIGNMENT
>
> check_a_343_> >> BEGINNING OF COMMAND
> check_a_335E> No alignment.
> recover____E> ERROR_STATUS >= STOP_ON_ERROR:        1       1
>
> Dynamically allocated memory at          finish [B,kB,MB]:      2200483
> 2148.909     2.099
> Starting time                                            : 2003/03/21
> 23:47:53.033
> Closing time                                             : 2003/03/21
> 23:48:02.202
> Total CPU time [seconds]                                 :       0.00
>
> ------ End of Forwarded Message