... 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:lsettimo@abo.fi Webpage URL http://www.abo.fi/~lsettimo --------------------------------------------------------
Modeller Care wrote:
> ------ Forwarded Message > From: Mario Garcia sbioi000@cib.csic.es > Date: Fri, 21 Mar 2003 16:53:17 +0100 (CET) > To: modeller-care@salilab.org > 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 : mario@cib.csic.es > 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