... 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