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FW: Modeller6v2 trouble



------ 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